Institutional Role Behind Civil-Military Equation

Institutional Role Behind Civil-Military Equation
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Muhammad Ismail Khan


In the political history of Pakistan, both civilian and military rulers have used intelligence agencies to further their goals. In this game of political snakes and ladders, the key players have employed intelligence outfits to spy on each other. Defining the purpose of an agency, this paper starts by identifying the main intelligence agencies of Pakistan which have played a role in the major developments of the country. These events, which are dealt with extensively in the next section, have tainted the image of the agencies. The focus is on the years following 1988 and the impact of developments in this period on the course of the country’s history.


Pakistan’s security agencies, not least its primary spy outfit the Inter- Services Intelligence (ISI), have caused grave international concern. Presently, the main worry of the global community is  the on-going war against terror, where there is a perception of alleged ISI collusion with the Taliban. Just as President Barack Obama announced the new Af-Pak policy, the US Chairman Joint Chief of Staff, Admiral Mike Mullen, expressed his concerns over the perceived support of Pakistan’s main military intelligence agency to radical elements.1 Such allegations have repeatedly been voiced after the US-led invasion of Afghanistan in order to flush out the Taliban from Kabul. The fleeing militants, it is argued, found their way to the tribal areas of Pakistan where the country’s secret agencies helped them establish safe havens.

Not only the United States, but nations within the south and central Asian regions are wary of alleged ISI support to militants inside their countries. New Delhi has repeatedly asked Pakistan to cut off ties with the militants which have supposedly carried out terrorist attacks in India. Similarly, in February 2009 Afghan intelligence officials blamed ISI for sponsoring the attack on the Justice Ministry in Kabul.2

Not only other countries, but also segments of domestic opinion in Pakistan have blamed the agencies for manipulating the political climate of the country in the past. Although their external role is not significantly different from those of other agencies of the world, it is their domestic activities that have imbued them with notoriety within the country. The political leadership as well as the intelligentsia has not, therefore, adequately defended the security services against external allegations.

Given the secretive nature of spy agencies, there is little they can do to defend themselves publicly. The ground further muddies as new allegations of the agencies’ external activities are made. This creates an impression of “rogue” elements within the ISI who act unilaterally instead of following the directives of the state. It is even suspected that several ideological elements within Pakistan’s security agencies influence state policies.

Army Staff (COAS), General Ashfaq Pervez Kayani, is lauded in the United States for his exemplary role in maintaining the army as a professional outfit. His gesture in resolving the confrontation between two of Pakistan’s political rivals has been termed as “the Kayani model.”3 Yet, it was during Kayani’s stint as Director General ISI4 that the escaping Taliban found safe havens in Pakistan’s tribal areas.

While there has been sufficient material5 on the ISI’s alleged support to Islamists or political players in the past, there is little that touches the institutional role and structure of the organization. What and who makes and draws the sympathies of these security services?

This paper looks beyond the role of the ISI. It starts by identifying the institutional role of intelligence agencies during important national events and ends up concluding that the sympathies of these outfits in Pakistan are a manifestation of civil-military imbalance in the country. In a country with a tense past in the civil-military equation, intelligence agencies are often used to play off one player against another. Moreover, it is the action taken on the spying, and not spying per se, which has made the agencies a dreaded entity in the society. Lastly, since Pakistan’s main military intelligence outfit is an external agency, the tussle between civilian-military intelligence has been restricted to domestic affairs. For civilian intelligence agencies, foreign policy is unfamiliar ground. Thus, the internal role of a military intelligence agency comes from the civil- military imbalance; the edge is in its being an external agency.


The  primary  purpose  of  any  country’s  intelligence  agency  is founded on the “state’s awareness and understanding of its strategic environment, gained by way of gathering and analyzing secret and open- source information.”6 The main task involves gathering of information, which is then analyzed so as to secure the state against any threat. Since, external groups are involved in acts against the state, the intelligence agency (IA) also works on counter-intelligence. Despite their various activities, it is in two basic areas, namely, the collection and analysis of information that    every IA concentrates. This overriding function of information gathering, research and analysis makes an IA almost like an academic institute. An IA’s involvement in covert actions often makes it a controversial organization. Pakistan’s IAs are, therefore, not exceptional.

As with many other states, Pakistan’s IAs can be divided as per geography and specialization. IAs which can be divided along the geographical domain include: external agency which is concerned with intelligence regarding external security, and internal agency which is concerned with intelligence regarding internal security. There are also specialized IAs within Pakistan whose primary task include intelligence on crime, drugs, etc. The overlapping of interests requires coordination and cooperation yet inter-agency conflict is also part of the matrix.7  (See Appendix ‘A’ for the structure of IAs in Pakistan.)

External agency

The Directorate of Inter-Services Intelligence, shortened as ISI, is involved in intelligence gathering and analysis of external threats. It also coordinates with foreign agencies in combating terrorism. In the

1980s, together with the Central Intelligence Agency, it was actively involved in the covert operations against the Soviet occupation forces inside Afghanistan. After the Soviet withdrawal, the ISI retained its links with the Afghan fighters. It is for this non-severance of links that the ISI is being accused presently by the international community. Moreover, within Pakistan, it has been involved in political dealings. The political leadership, therefore, is equally skeptical of the agency. Recently, it appeared as a dreaded organization in the infamous “missing persons” case wherein it was revealed that people associated with ISI were involved in the abduction of several Pakistani nationals.

In terms of line of communication, although the ISI comes under Prime Minister, its de facto status is under Chief of Army Staff (COAS). It reports to both the Prime Minister and the COAS. Reportedly, having a staff of more than 10,000(other than informants)8, the ISI has been mostly headed by a Lieutenant General though in its early days the head of the agency was an officer of the rank of Brigadier. It is divided into the following departments:9

1.  Joint Intelligence X (JIX) – acts as a center which coordinates with other wings; it also provides intelligence and threat assessments.

2.  Joint  Intelligence  Bureau  (JIB)  – considered  as  the  most powerful bureau; one of its subsection was devoted to India. Since this bureau is also responsible for political intelligence, within ISI” cannot be denied.

3.  Joint       Counter         Intelligence        Bureau (JCIB)    – conducts surveillance of Pakistani diplomats stationed abroad; it is also responsible for conducting intelligence operation in the Middle East, South Asia, China, Afghanistan and the Muslim republics of the former Soviet Union.

4.  Joint Intelligence / North (JIN) – responsible for Jammu and Kashmir operations, such as infiltration, propaganda, and other clandestine activities.

5.  Joint Intelligence Miscellaneous (JIM) – is believed to be conducting espionage in foreign countries, including offensive intelligence operations.

6.  Joint  Signal  Intelligence  Bureau  (JSIB)  – responsible  for signal intelligence along the border with India, and to “provide communication support to militants in Kashmir.”

7.  The  Special  Wing  – responsible  for  liaison  with  foreign intelligence and security agencies; it is this wing which is reported to have links with the Taliban. This wing may possibly be under JIM.

8.  Joint       Intelligence  Technical– intelligence such as gadgetry.

10.  Responsible               for          technical Internal agency

Intelligence Bureau, abbreviated as IB, is Pakistan’s internal IA. It was largely a police organization and still retains this character by and large. Although a part of the Ministry of Interior, it also reports directly to the Prime Minister. The primary job of IB is intelligence gathering within the country, which may include terrorists, foreign intelligence agents, etc. Nonetheless, it has also been used for political manipulations in Pakistan.


The Pakistan, army, navy, and air force have their own intelligence agencies. They are involved in intelligence gathering as per respective requirements. Military Intelligence is the army’s primary IA. Since Pakistan has for more than three decades been under military rule, this agency has often made headlines for political reasons.


Pakistan’s law enforcement outfits also have intelligence cells though these are normally described as “investigation” departments or agencies. Such IAs, which deal mostly with crime,  are all civilian and come under the Ministry of Interior. Intelligence is gathered through the Central Investigative Department and the Federal Investigative Agency

– both are policing organizations. Recently, they have been involved in probes against militants operating inside Pakistan.


There is also an intelligence unit within the Anti-Narcotics Force, which comes under the Ministry of Narcotics Control. The unit is tasked with gathering information in order to pre-empt drug trafficking.

Law enforcement agencies

Though the activities of law enforcement agencies (LEA), such as the police, should be confined to punitive action against criminals, they have also developed their own intelligence apparatus.  In Pakistan paramilitary agencies notably the Frontier Corps and the Rangers also fall within the ambit of LEAs. While IAs have become notorious for their power and political interference, the role of the LEAs has been no less controversial.


Formation and growth (1947-1977):

Given the tense equation between the rulers and the ruled during the colonial era, the British resorted to the use of stringent, if not repressive, internal surveillance. The intelligence apparatus which Pakistan inherited from the British came to be associated with internal intelligence. Along the lines of the division of other resources, the pre- partition Intelligence Bureau (IB) was bifurcated between Pakistan and such as the  CID, had become dreaded bodies.

Almost immediately after partition, war broke out between Pakistan and India over Kashmir. The need for an agency to coordinate intelligence among the three branches of the armed forces was soon realized.12 Thus in July 1948, Pakistan’s then Deputy Chief of Staff, Maj. General R Cawthome, established the ISI as a small organization under the General Headquarters. Its placement below the GHQ ensured that from the very beginning it would be army-dominated and, as such, it reported to the commander-in-chief.

In 1958, Pakistan experienced its first military rule. The ISI along with all other agencies fell under the authority of the President and C-in-C, General Ayub Khan. Most of the intelligence structure at that time was used for domestic spying, particularly against opposition politicians. There was a close surveillance on politicians during the 1964 elections; the ISI and the IB were growing “in stature and power.”13 This internal obsession proved detrimental to the focus on external concerns.

Pakistan’s major intelligence crisis came in the form of the 1965 war with India. The war seemed to have been planned with pre-conceived notions instead of taking alternatives and fall-back positions into consideration. For instance, after the launch of operation Gibraltar into Indian occupied Kashmir, there was no revolt among the Kashmiris as had been anticipated. It was in the expectation that an uprising would spontaneously materialize that the war was started. Moreover, the possibility that India could open up the southern sector by crossing the international border in Sialkot or Lahore was also not factored. Setting aside the policy miscalculations, the ISI proved ineffective in locating an armored division of India during the war. Headed by Brigadier Riaz Hussain, the ISI’s assets in the Indian sector proved ineffective thereby “blinding”14 it to the developments. After the war, a committee was established under General Yahya Khan to look into the working of the agencies. The nominal control of the ISI shifted to the Ministry of Defense.

By 1968 it became increasingly apparent that Ayub Khan’s days were numbered. He soon stepped down and was succeeded by General Yahya Khan. The latter organized general elections in 1970 but was reluctant to accept the outcome. Earlier, he had tried to use the ISI to infiltrate Bengali politicians but this did not work out. During the elections, Yahya’s cabinet regularly received “briefings”15 from the head of IB. His military operation in East Pakistan and the subsequent war with India proved disastrous as it ended in the creation of Bangladesh.

From a purely intelligence perspective, it is obvious that this was another complete intelligence failure in correctly assessing the ground situation. Not only were the sympathies of Bengalis discounted but the success of military operation was overvalued.

After Yahya Khan, Zulfikar Ali Bhutto became the President and later Prime Minister of Pakistan. Bhutto’s decision to appoint Zia-ul- Haq as the army chief was influenced by General Ghulam Jilani Khan, his appointee as DG ISI. Interestingly, it is Bhutto who is credited with creating the notorious “political cell” within the ISI.16 For his opponents, the dread came from Federal Security Force (FSF,) a paramilitary organization formed by the government. Opponents of Bhutto decried the use of FSF for political manipulation. It is believed that the aim of the FSF was “to enable a civilian government to avoid seeking the assistance of the armed forces in dealing with its responsibilities and problems.”17  Whether or not the FSF was established to “counter the influence of ISI,”18  it became an instrument for the accretion of power in the office of the prime minister.

The access to IAs and LEAs did not help empower Bhutto in the context of the civil-military equation. When Zia asked Bhutto to withdraw the surveillance of “civilian IB on army officers,”19  Bhutto complied by replacing an IB chief.20 Bhutto was removed from power in a military coup in 1977; two years later he was sent to the gallows. Zia retained Gen. Jilani after his retirement and dismantled the FSF.

Spectacular rise (1980s):

The emergence of the ISI as a larger-than-life agency is derived from 1988) that the IAs, and in particular the ISI, became actively involved in changing the geo-political environment.

Zia stage-managed the rise of certain politicians who, in turn, helped him stay in power. The IAs were used to garner support for Zia and his policy of Islamization as well as to demonize Bhutto’s Pakistan People’s Party (PPP.) Individuals who had fallen foul with Bhutto rallied around Zia. Thus the IAs played an active role in providing a joint political platform to the anti-Bhutto constituency. For instance, since Bhutto had nationalized industries during his tenure, the support of many industrialists was sought. Army and intelligence officers played a prominent role in this endeavour.21

What lead to the ISI’s spectacular growth was the war in Afghanistan. Soon after the Soviet invasion of Afghanistan, Pakistan came into the limelight. The ISI, with the help of the Central Intelligence Agency (CIA), funded the militants known as Afghan mujahideen. The initial secrecy maintained by the United States and the importance attached to Pakistan gave the ISI a free hand in Afghanistan.

The Afghan war imbued the ISI with a decisive say on key foreign policy issues.  It was during this period that the direct link between Saudi Arabia and the ISI was established.22 The latter was thus able to secure mind-boggling amounts of financial assistance to pursue the jihad without questions being asked.

The free hand given to the ISI remains incomprehensible. The latter established close links with the mujahideen groups. All the funds, weapons and ammunition for the Afghan resistance were thus channeled through the ISI. Once the finances were secured, it was the “ISI and not Army that took on the principal role for the execution of the covert war against the Soviets.”23  This was fully endorsed by Zia whose protégé, General Akhtar Abdur Rehman, headed the ISI as its director general.

General Zia-ul-Haq and General Akhtar Abdur Rehman both died in a plane crash in 1988. Zia was succeeded by General Mirza Aslam Beg as COAS; Rehman by General Hameed Gul. Democratic control or control of democracy? (1988-1999):

The involvement of IAs, especially the ISI, in the affairs of the state has had a negative impact and according to author Shuja Nawaz:

“The active involvement of the army high command and intelligence services, particularly the ISI, in the conduct of the Afghan war, the ISI’s direct and unfettered access to overseas financing from US CIA and private and official Saudi sources, and involvement in the making and breaking of domestic political parties and alliances, had changed the equation between the civil and military. This involvement and financial autonomy of sorts also gave the ISI a permanent role in foreign policy.”24

Bhutto wins –

After Zia-ul-Haq’s death, fresh elections were to be held.  Zulfikar Ali  Bhutto’s  Pakistan  People’s  Party  (PPP),  led  by  his  daughter, Benazir Bhutto, decided to take part in the polls. Already a mainstream force, Bhutto’s party had become even more popular despite years of persecution during the Zia-ul-Haq era. The assessment was that Benazir Bhutto would secure a landslide victory if the elections were free and fair.

For this precise reason, the then DG ISI, General Hameed Gul, is said to have been against the holding of elections.25  Nevertheless, the Army chief, General Mirza Aslam Beg, and the President, Ghulam Ishaq Khan, decided to move ahead with the scheduled elections. This demonstrated that despite its growing stature, the ISI could still not always impose its will.

However, in order to neutralize Bhutto’s popularity, an alliance of right-wing parties, known as the Islamic Democratic Front or the IJI26, was cobbled together through the active involvement of the DG ISI and the Army Chief.27 was known primarily as a wealthy Saudi businessman, is said to have provided funds, according to an English newspaper published from Lahore, through the ISI for disbursement to the IJI.28 The ISI’s links with key figures in Saudi Arabia had developed during the Afghan war.

Despite these machinations, the PPP won sufficient votes to form the government at the center while the IJI became the main opposition party. The latter was, however, able to form the government in the Punjab, Pakistan’s largest province. Given the federal structure of the country this posed serious difficulties. Thus from day one, the journey towards democracy was anything but smooth. In this period the IJI asked the ISI for its support and this, in turn, pitted the latter against the PPP.

Pakistan’s military strategy is India-centric and, because of this, it sought to establish strategic depth in Afghanistan after the Soviet withdrawal from that country. The perception was this was not supported by the PPP. Thus even after winning the elections, Benazir Bhutto was asked to take the COAS into confidence on all security matters and not to touch “sensitive” issues such as India, Afghanistan, nuclear and defence policy.29 Hence, despite being the prime minister, she had little say in foreign affairs.

While Bhutto seemed to have accepted these restrictions, her problems did not end. Byzantine intrigues, with the connivance of the IA, to destabilize her government were engineered. One such event was the infamous “Operation Midnight Jackal” through which attempts were made to buy off her supporters. Under the circumstances the Prime Minister sought to set up a commission to    reform the intelligence agencies. Benazir Bhutto was also convinced that most of her troubles emanated from one particular individual, General Hameed Gul, she therefore had him removed from the post of DG ISI and appointed, Shams-ur-Rehman  Kallue,  a  retired  General,  in  his  place.  Hameed Gul’s removal demonstrated yet again the pivotal role of DG ISI in the country’s politics.  Kallue’s appointment was aimed to sever the links between the army and the ISI.

It is interesting that at this juncture, the COAS started seeking advice from the DG of Military Intelligence, General Asad Durrani. Thus, MI became the “ears and eyes” of the army.30 On the other hand, the ISI under Kallue, who acquired the nickname “no clue,” proved ineffective and was of no use to the Prime Minister. Her government was unceremoniously dismissed in 1990 after remaining barely two years in power.

Sharif leads –

After the dismissal of the Benazir Bhutto government, fresh elections were held. Though the tables were turned the key players remained the same. The PPP became the main opposition party and Nawaz Sharif formed the government. The army and the intelligence agencies are said to have played a helpful role in clinching Sharif’s victory.

During these elections, the COAS, General Mirza Aslam Beg, is reported to have given 140 million rupees to the new DG ISI, General Assad Durrani,31 for distribution among anti-PPP candidates. The funds were provided by the CEO of the Mehran Bank, Yunus Habib. Whether or not, bin Laden or any other rich mujahideen donated money to the IJI in 1990 (as they did in 1988) is not clear. In 2006, Qazi Hussein Ahmed, an IJI leader, said in an interview that when he was approached by bin Laden to support IJI in the 1990 elections, he “disagreed with his method.”32 Whether or not others also disagreed is not known; what is certain is that unlike 1988, the ISI did not act as a mediator.

It was not till 1994 that General (Retd.) Naseerullah Babar, a PPP leader, revealed how the ISI had disbursed money among politicians. In 1997, a case was filed by Air Marshal (Retd.) Asghar Khan; during the hearing of the case, General Beg admitted the supply of funds to political leaders.

Pakistani columnist, Ardeshir Cowasjee, quoted Beg’s confession to the Court in Dawn:

“In 1990 when the money was donated by Younas Habib, ISI was acting under the directions of higher authorities. As chief of the army staff at that time, when I was informed of this matter my only concern was that the money received by the ISI was utilized properly and an account was maintained and beyond that I had no concern with the money.”33

And that,

“Although the director-general, ISI, is an officer in uniform but the chief of army staff has no authority to take action against him. The head of ISI was a person from army of which I was head at the relevant time.”34

However, Durrani later signed an affidavit that he was asked by General Beg to provide “logistic support”35  to the politicians through “businessmen of Karachi.”36 The case is still pending in the Court.

After winning the elections, the IJI leader, Nawaz Sharif, became the Prime Minister of Pakistan. The President and the COAS, who had earlier colluded in the dismissal of Bhutto’s government in 1990, remained the same. General Beg retired soon afterwards and was succeeded by General Asif Nawaz as COAS. Though Nawaz Sharif had been supported by the military, his relations with both the army as well as the President were tense. For his part, General Asif Nawaz wanted to depoliticize the army and, as such, did not interfere in politics.

After Kallue, General Durrani (DG MI) was made DG ISI.  Sharif replaced him with General Javed Nasir a born-again Muslim with a pan Islamic worldview.37 Other than supporting Islamic groups in China and Philippines, he is also alleged to have supplied arms to the besieged Bosnians in the Serb siege.38  During his tenure the ambience at ISI was “a strange non-military atmosphere” where the “corridors were filled with bearded officers in civilian costumes.”39  The next DG ISI, General Qazi, revamped the ISI on the orders of the COAS – making its operations more professional.

Earlier, General Nasir was removed after a new COAS, General Waheed Kakar, took over. Kakar’s predecessor, General Nawaz, had died mysteriously. Meanwhile, the rift between the President and the Prime Minister was growing, bringing in the army once again.40 In 1996, without taking over the country, General Kakar asked the President and the Prime Minister to quit and also called for fresh elections. In a country where the President can dismiss an elected Prime Minister, such an arrangement came to be known as the “Kakar formula.”

BB returns –

Benazir Bhutto won the general elections in 1994 and appointed a party-member, Farooq Leghari, as president. General Kakar was offered an extension by Bhutto, but he refused. Upon his retirement, General Jehangir Karamat took over as COAS.

Since her first government was dismissed within two years, Benazir went the extra mile to keep the power brokers contented during her second term. Once bitten twice shy, she fully cooperated in the security vision of the country that consisted of deterring India by securing Afghanistan and the nuclear weapons.

There  were  however  some  interesting  differences  between  her first and second terms. For instance, the Ministry of Interior became more important. The Minister of Interior, Naseerullah Babar, although a retired general, was a party loyalist. Along with other key civilian IAs and LEAs, his ministry started an operation in the port city of Karachi.

Moreover, it was during her second government that Taliban started receiving support from Pakistan. The question whether it was Pakistan that master-minded the creation of the Taliban remains unanswered. What, however, is relatively certain is that the moment Taliban emerged as a force, Pakistan established close links with the movement. Since the 1980s, Pakistan had supported the mujahideen and this continued even after the withdrawal of Soviet forces from Afghanistan. It was General Babar who sought the help of Taliban to secure the release of some Pakistani trucks that had been captured by the warlords. Later, particularly after 9/11 the mujahideen switched to the Taliban raising suspicions that they were supported by the ISI.

In her second term, Bhutto used the Interior Ministry to consolidate political power. The LEAs and IAs were thus made answerable to the Prime Minister. She appointed her trusted people to the Federal Bureau of Investigations43  and Intelligence Bureau. According to FAS, “the appointment [of DG IB] precipitated a major crisis in the Pakistani state apparatus, because Benazir then began using the IB chief to erode the once all powerful ISI’s base.”44 As events would show this did not help her. She was sacked in 1996 – this time, by her own handpicked President.

Sharif returns –

Sharif won the next general election. Not only did he appoint a loyalist as President, he also amended the constitution, as he had the required parliamentary majority. This was consequential because the President no longer had the power to dismiss an elected Prime Minister. To further consolidate his position, he appointed General Ziauddin, a non-professional army-man from the Engineering Corps, as DG ISI.

During Sharif’s second term, Najam Sethi, editor of The Friday Times, a leading weekly, was picked up from his house. Earlier, Sethi, while in India, had criticized the Sharif government for corruption. While there was confusion over his abduction, he was interrogated by ISI. The Lahore High Court refused to take up the case as it was a military affair – something beyond the jurisdiction of the civil courts. When Sethi’s wife appealed to the Supreme Court, its response was that the case would be heard by first deciding the status of ISI “once and for all”46 and if it is a military affair then, the Court would have no jurisdiction under Article 199 (3). Nonetheless, it remarked that “prima facie, the ISI is not part of the army.”47

The highhandedness of the Sharif government was again apparent in the Rehmat Shah Afridi case. The latter, who was the editor of the Peshawar-based Frontier Post was nabbed on 1 April 1999 by the Anti- Narcotics Force for allegedly being in possession of 20 kilograms of hashish. According to Afridi, he was arrested for his paper’s criticism of Sharif’s administration. After his release, he stated that his paper had published a report that then “DG of ANF and some army officers were involved in drug smuggling.”48

In 1999, Pakistan went to war with India in Kargil, causing serious rifts within the country’s polity. It is said that the DG ISI was unaware of the operations; MI was colluding with the Sharif-appointed COAS, General Pervez Muharraf. Later, Sharif was blamed for caving in to international pressure by agreeing to the withdrawal of troops. After the war, Sharif began to distrust Musharraf who, according to Sharif, had never informed him of the Kargil misadventure. Eventually the prime minister decided to dismiss Musharraf. On the evening of 12 October 1999, while Sharif was in the process of formalizing the appointment of General Ziauddin as the new COAS, General Musharraf took over the government through a coup.

Military returns (1999 – ):

With the October 1999 coup, the role of intelligence reverted yet again to supporting military rule. Musharraf appointed his favorites to the key intelligence slots – such as in the ISI and MI. These generals had been instrumental in staging the coup as Musharraf was returning to Pakistan from a visit to Sri Lanka at the time.

Two years later 9/11 occurred and the United States became ever more assertive as it embarked on its global war on terror. The choice for Pakistan was stark. Washington had made it clear with the formulation “either you are with us or against us.”

However, there were voices of resistance within the ISI. When Musharraf was confronted with intelligence officials who did not want to shun the Taliban, he purged the agency of such elements. These included DG ISI, General Mahmood who was considered a staunch Taliban supporter and was present with American Congressmen when 9/11 happened. On his return to Pakistan, Musharraf asked General Mahmood to convince Taliban to hand over bin Laden.50 However, it is said that Mahmood asked Mullah Omer to resist the invading forces.51

There are also reports of Mahmood providing $100,000 to 9/11 master- mind, Muhammad Atta, through a middle man, Omer Sheikh.52 The Wall Street Journal reporter Daniel Pearl reported the call made by Mahmoud to Sheikh. Sheikh was subsequently arrested by the ISI for the murder of Pearl. Later on, the FBI is said to have interrogated Mahmood for his role.53

As the war raged in Afghanistan, the ISI became the front line player once again. Pakistan helped the United States in arresting and deporting Taliban leaders.

The escaping Taliban found sanctuaries in the tribal areas of Pakistan and were said to be    actively supported by the ISI. Later, the world would condemn the ISI for supporting the militants. This continued and General Musharraf acquired the reputation of being a “double dealer.” The resurgence of the Taliban in the tribal areas happened after 2004, when General Ashfaq Kayani was made DG ISI.

Politically too, the ISI became increasingly involved. In 2002, parliamentary elections were held in which the pro-Musharraf parties won a majority. These elections, admitted later by ISI’s political cell head General Zamir, were rigged in favor of Musharraf’s favorites.54

According to General Zamir, he was asked by Musharraf to do so.55

The ISI’s alleged role in abducting civilians was no less controversial. Imbued with special powers, the agency picked up people on the pretext that they were terrorists. The case of missing persons was taken up by the Supreme Court. Much to the anger of General Musharraf, the top judge took keen interest in this issue.  During hearings, it became apparent that many people were abducted for no good reason. A case in point was of a person named Imran. According to The News, a Lahore- based newspaper, “the counsel for Imran had told the bench that Imran had an affair with a girl who was a relative of a brigadier in the ISI.”56

This showed that the ISI had grown in size with an added responsibility of acting like paramilitary unit or LEA.

Power blinds. This was as true of Nawaz Sharif during his second term as it was of Musharraf. In March 2007, Musharraf suspended the Chief Justice of the Supreme Court and this ignited a country-wide agitation for his restoration. This finally came about in March 2009 by which time Musharraf was no longer the president of the country.

Prior to this Benazir Bhutto and Nawaz Sharif, who had both been in exile for several years, returned to Pakistan.    Upon her return, the convoy of Benazir Bhutto was attacked. Although she survived the first attack, she died in the second one. When she was attacked the first time in 2008, she blamed some of the leaders of the then ruling PML (Q) as well as individuals associated within the intelligence.57

Post-Musharraf period–

In 2008, fresh elections were held. Bhutto’s party won in the Center with Sharif’s party forming the government in the Punjab province. While the Punjab-Center setup was nearly the same, the only apparent difference was the absence of animosity between the two parties.

Before Musharraf’s ouster, General Ashfaq Pervez Kayani was made COAS after taking the key political actors into confidence. That both Bhutto and Musharraf expressed confidence in his appointment showed his professionalism.58

The new civilian government unsuccessfully tried to rein in the ISI. On 26 July 2008, a notification was issued stating that the ISI would be under the Ministry of Interior.59  However, this was staunchly resisted by the army forcing the government to backtrack and announce that the original “notification has been misunderstood.”60

In November 2008, India’s port city Mumbai was attacked. As a gesture of cooperation, President Zardari asked DG ISI, General Pasha, to go to Mumbai. However, when this unleashed severe criticism in the media and also resulted in expressions of resentment within the military establishment, the ill-thought-through initiative was withdrawn.

As in previous civilian governments, the Ministry of Interior is again in the limelight. As for the fight against terrorism, the organizations associated with MoI, such as CID and other policing IAs, have also been active. Given the fact that policing IAs are mostly reactive outfits and without adequate means, such a division often results in wastage of time and resources. The present war against terrorism calls for close coordination between all IAs. The challenge is formidable as terrorism as the foremost external and internal threat that the country faces.

As in the past, it is the civilian IAs and LEAs that are being misused for political ends.   For example, the federal government imposed Governor Rule in the Punjab, a province ruled by Sharif’s party, to curb the lawyers’ movement for the restoration of the deposed judiciary. It is believed that the Lahore Chapter of the Intelligence Bureau played a key role in the imposition of the rule.61


Civil-military imbalance:

The political activities of the intelligence agencies in Pakistan reflect the civil-military imbalance in the country. In this equation, civilian rulers have opted for civilian IAs while military rulers   have used the military IAs.

The case of ISI is most interesting; although known as a “semi- military” organization under the authority of the Prime Minister, it is subservient to the COAS in reality. Most of ISI’s cadre also comes from the army. Whenever a case involving ISI has been heard in Court, the first concern has been over its status.62

It is for this reason that the civilian leadership had resorted to using civilian IAs as well as LEAs. Although they are subjected to parliamentary questions, the over-arching role of the Ministry of Interior or civilian intelligence units indicate the desire to curtail the influence of the ISI and indirectly, the military. Since the law-enforcement agencies (LEA), like the police force, also come under the Interior Ministry, this ministry often assumes a larger role under civilian rule.

Politicians dread the ISI and call it a state within a state. In 1997, when the Mehran Bank scandal was being heard in the Supreme Court, former COAS Beg clearly said that he “cannot take action against DG ISI.”

Since the ISI is technically under the Prime Minister, its activities without his approval and knowledge cannot be justified. Politicians often criticize the role of generals in the rigging of elections and are also suspicious of civilian intelligence for political manipulations. For instance, the PPP leaders disliked the former Director General of the IB for his role in the creation of a pro-Musharraf party and his ties with Islamists.63

At another level, while the perception was that the ISI was capable of generating independent revenues from sources such as narcotics, foreign financiers and domestic bankers, these lucrative avenues of funding were no less coveted by elements within the political leadership.

On the other hand, critics accuse the civilians of misusing LEAs or IAs. This has included usage of CID to ANF for personal ends. Just as military rulers appointed favorites in ISI, civilians too have appointed their protégés in the civilian apparatus.

Individuals associated with civilian and military IAs have admitted their involvement in politics. that emerges is that such agencies act independently. There is, nevertheless, a difference of opinion about this. Individuals associated with military intelligence institutions, like the ISI, maintain that they are merely “operators” and not “policymakers.”

Internal-versus-external affairs:

In its purest form, intelligence is concerned with information gathering based on which action is taken.  Domestic intelligence is largely associated with LEAs, whose activities can at times be brutal, harsh and extreme. That the ISI became notorious for abducting citizens during Musharraf’s time shows the evolution of an IA into a semi-LEA outfit.

Civilians have used civilian agencies to ensure the writ of the state. Political governments have tried to curtail the ISI’s role by relying on civilian IAs and LEAs. While civilian intelligences have only remained within the domestic domain, the ISI’s domestic spying seems to be only an extension of its primary task of external intelligence.

Theoretically, the ISI is an external IA and this gives it an edge over its civilian counterparts which are often crime-centric.

Sources include:

  1. Background Paper on “The Structure and Role of Intelligence Agencies” by Lt. Gen Asad Durrani for Pakistan Institute of Legislative Development (PILDAT.)
  2. Websites of the ministries.


1.                   Mark Mazzetti and Eric Schmitt, March 29, 2009. “U.S. Says Agents Of Pakistan Aid Afghan Taliban.” The New York Times.

2.                   Sangar Rahimi and Carlotta Gall. March 20, 2009. “Pakistan Accused of Links to Kabul Attacks.” The New York Times. < asia/20afghan.html>

3.                   Jehangir Karamat, 2009. “The Power of People Power.” Spearhead Research. <http://>

4.                   From 2004 to 2007, Kayani was Director General ISI. It was during this time that insurgency started in tribal areas and Dr. AQ Khan Scandal was exposed.

5.                   On general idea about Pakistan, see: Stephen Cohen’s The Idea of Pakistan. On books about the dominance of military and religion in Pakistan, see: Husain Haqqani’s Pakistan: Between Mosque and Military or Hasan Abbas’ Pakistan’s Drift into Extremism. On links with Islamists, see: Zahid Husain’s Frontline Pakistan: The Struggle with Militant Islam. On Afghan jihad, see: Steve Coll’s Ghost Wars: The Secret History of the CIA, Afghanistan, and bin Laden, from the Soviet Invasion to September 10, 2001; On Taliban, see: Ahmed Rashid’s Taliban: Militant Islam, Oil and Fundamentalism in Central Asia; Ahmed Rashid’s Descent into Chaos: The U.S. and the Disaster in Pakistan, Afghanistan, and Central Asia; On military, see: Shuja Nawaz’s Crossed Swords: Pakistan, Its Army, and the Wars Within. For personal memoirs of the key players, see: Musharraf’s In the Line of Fire: A Memoir; Benazir Bhutto’s Daughter of the East; Benazir Bhutto’s Reconciliation: Islam, Democracy and the West.

6.                   DCFA Backgrounder, 2006. Intelligence Services; Democratic Control of Armed Forces, pp. 1.

Full  backgrounder  on  intelligence  can  also  be  accessed  at:  <


7.                   Such conflict may raise suspicion with regards to coordination. For instance, Pakistan’s external IA funded its war on drug money – against which a specialized IA works on.

8.                   See:

9                    See:

10   Frédéric Grare. Reforming the Intelligence Agencies in Pakistan’s Transitional Democracy. Carnegie Endowment for International Peace (2009); pp. 16

11   Hassan Abbas. 2007. Pakistan’s Drift into Extremism. Pentagon Press; pp. 245

12   Sean P. Witchell, ‘Pakistan’s ISI: The Invisible Government’, International Journal of Intelligence and Counter-Intelligence, Vol 16(1), (Spring 2003) pp 374-375.

13   Nawaz, Shuja. 2008. Crossed Swords: Pakistan, its Army and the Wars Within. Oxford University Press; pp. 255.

14   Sean P. Witchell; Ibid, pp. 376.

15   Nawaz. Ibid. pp. 256

16   It was shared by a future COAS, General Beg, in a Supreme Court case in 1997.

17   Attributed to Bhutto; quoted by Ardeshir Cowasjee in his article. See: Cowasjee, “The missing chapter,” Dawn (June 28, 1997)


19   Nawaz. Ibid. pp. 349

20  The replacement of a single person at top shows the strength associated with such a person. This would be repeated later on, too.

21   These industrialists included Nawaz Sharif, who was picked up by General Jilani, former chief of ISI. Sharif would later lead a mainstream political force.

22   Nawaz. Ibid. pp. 372

23   Nawaz. Ibid. pp. 373

24   Nawaz. Ibid. pp. 360

25   Nawaz; Ibid. pp. 412-413

26   Its original name in Urdu is Islami Jamhooria Ittehad.

27   Nawaz; Ibid. pp. 411-413.

28   Daily Times Monitor. “Nawaz Sharif met Osama three times: ISI officials.” Daily Times, Lahore (June, 23,2005) See: <


29   Exact points included: no change in the Afghanistan policy, nuclear policy, defense policy, no administrative meddling in civil service and not harassing General Zia’s family. See: Nawaz; Ibid; pp. 415

30   Nawaz; Ibid. pp. 426

31   After Kallue’s exit, Durrani was called in to head ISI.

32   Editorial. “Qazi Hussein and Osama bin Laden.” Daily Times (March 20, 2008) See:\03\20\story_20-3-2006_pg3_1

33   Cowasjee, Ardeshir. “We never learn from history-3” Dawn (August 11, 2002)

34   Cowasjee, Ardeshir. Ibid.

35   Ardeshir, Cowasjee. Ibid.

36   Ardeshir Cowasjee. Ibid.

37   Abbas calls Nasir’s view as “worldview jurisdiction for ISI.” Abbas; Ibid. pp.148

38   Abbas; Ibid. pp. 148

39   Nawaz. Ibid. pp. 467-468

40   This power was bestowed to the President by General Zia.  Benazir Bhutto was also a victim of same power.

41   Presently too, the then-Minister General Babar often takes credit for establishing peace in Afghanistan by nurturing Taliban.

42   There is disagreement over who was the first to contact Taliban – ISI or Babar.

43   Rehman Malik, the present MoI, was made chief of FIA.

44   See:

45   ISPR, known as Inter-Services Public Relations

46   Rafaqat Ali. “ISI status to be decided once for all: Saiduzzaman.” Dawn (May 22, 1999)

47   Rafaqat Ali. Ibid.

48   Staff Reporter. “Rehmat Shah Afridi freed on parole” Dawn (May 25, 2008) See: http://

49   Rashid, Ahmed. 2008. Descent into Chaos: The United States and the Failure of Nation Building in Pakistan, Afghanistan, and Central Asia. Viking Adult

50   Musharraf, Pervez. In the Line of Fire. Simon& Schuster (2006)

51   Mir, Amir. The Fluttering Flag of Jehad. Mashal Books (2008)

52   Meacher, Michael T. “The Pakistan Connection.” Guardian (2004)

53   Mir. Ibid. 2008

54   Umer Cheema. “The man, who rigged 2002 polls, spills the beans.” The News (February

24, 2008) See: <>

55   Umer Cheema. Ibid. 2008.

56   Muhammad Qasim. 2008. “Five more missing persons traced, SC told” The News (May

26, 2007)

57   These included General Hamid Gul, former DG ISI, during Bhutto’s time from 1988 to 1990; and Brig (Retd.) Ejaz Shah, the then-DG of Intelligence Bureau.

58   It is important to realize that in a bumpy journey of Pakistan’s political history where military has taken the driving seat, professionalism is associated with lack of desire to rule directly – even if the COAS has influenced on key political events.

59   Raza, Syed Irfan. “ISI, IB put under interior division’s control.” Dawn. (June 27, 2008) See:

60   Report; “Notification regarding ISI has been misunderstood: PID.” The News.

61   Tariq Butt.  “Intelligence Bureau trying to catch multilingual terrorist chatter” The News

(May 25, 2009) See: <>

62   The cases involving hearing of Sethi’s abduction (1999) and missing persons (pending) revolved with the legal authority of ISI.

63   Hamid Mir. “Why Benazir points finger at IB chief.” The News (October 20, 2007) See:


64   As DG of FIA, he worked actively with Bhutto, when she was PM. He was hounded after Bhutto’s fall. Later on, he stayed in UK as security advisor of Bhutto.