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Aug 11, 2008 | 19:03 GMT

18 mins read

Special Report: Inside Pakistan's Shadowy Intelligence Agency


UPDATE, May 2011: In light of the death of Osama bin Laden, questions about the ISI have been asked. This body of work remains our best piece on the issue and the content is still relevant.


Pakistan's premier intelligence agency, the Directorate of Inter-Services Intelligence (ISI), is now more than ever at the center of an international controversy over its ties to Islamist militants. The Pakistani state must overhaul the ISI in order to handle foreign (particularly U.S.) pressure, combat a growing jihadist insurgency at home and reverse the current crisis of governance. But the ISI's historical evolution into a large, powerful and autonomous entity renders such a task extremely difficult.


Pakistan's Directorate of Inter-Services Intelligence (ISI), the country's main intelligence agency, played a key role in the rise of transnational jihadism by cultivating Islamist militants for its own strategic purposes in Afghanistan and Kashmir. The Pakistanis — especially the ISI — perceived the United States' lack of interest in Afghanistan after the Soviet withdrawal as a green light for them to do as they pleased in the country, and in neighboring India. In the meantime, al Qaeda was pursuing its own agenda, and many of Pakistan's own proxies were becoming more and more autonomous. Finally, the post-9/11 global security environment ruptured the ISI-jihadist relationship. Much more recently, the ISI appears to have lost control of many of its former proxies as well as itself.

A growing Taliban movement assuming control of various parts of Pashtun-dominated northwestern Pakistan, increasing U.S. unilateral operations against al Qaeda and Taliban elements in the same area, and Islamist militant attacks in neighboring Afghanistan and India all have one common denominator: the ISI.

Suicide bomb attacks — mostly against Pakistan's security services — and the erosion of the writ of the government in Pakistan's tribal belt and many areas of the North-West Frontier Province are taking place because the ISI's former assets are able to use their ties within the directorate to sustain their operations. Jihadists fighting the Pakistani state are able to exploit the Pakistani army's inability and/or unwillingness to completely sever ties with Islamist militants, as well as the significant presence of Islamist sympathizers within the ISI.

Meanwhile, the United States — after long suspecting elements within the ISI and other parts of the military of colluding with al Qaeda and Taliban militants — has moved toward taking overt unilateral action against Pakistan-based jihadist forces. The manner in which Washington, including President George W. Bush himself, officially has come out questioning the ISI in recent weeks is unprecedented. Until now, the Bush administration never directly criticized the directorate and other institutions within the army, instead relying on media leaks to put pressure on the Pakistanis to rein in the ISI. Should things get out of hand, it is not beyond the pale that Washington could officially designate the ISI as a terrorism-supporting entity (along the lines of the October 2007 U.S. executive order against Iran's Revolutionary Guards Corps).

At a time when the Pakistani state is trying to contain runaway insurgency on the domestic front as well as maintain its status as a frontline ally in the U.S. war against Islamist militants, there is evidence implicating the ISI in large-scale attacks in both Afghanistan and India. The fact that Pakistan is the target of Islamist militants and can still commission attacks in both its neighboring countries speaks volumes about the nebulous nature of the ISI-jihadist nexus. While the intelligence service has clearly lost control of a significant number of militant Islamists, there are others which it still controls.

The jihadists never were a monolithic entity, but over time the ISI also has become an extremely complex organization fraught with internal contradictions. As with any other foreign intelligence service, its opaque nature creates conditions that are ripe for operations that might not necessarily have official sanction. Exacerbating this situation is the fact that the Pakistani state lacks any institutional checks that could help maintain oversight over ISI operations.

In addition to being an institution within the country's military establishment, the ISI also plays a key role in domestic politics — keeping the country's political parties in line — which gave it further immunity from any oversight. While it has kept civilian forces and ethnonationalist movements under wraps, the ISI as a body has been compromised by the relationship it has cultivated with Islamist militant groups over the last three decades or so.

The Pre-Islamism Years

The ISI was created in 1948 by Maj. Gen. William Cawthorne, the then British Deputy Chief of Staff of the Pakistani army. It was designed to address the intelligence failures of the existing directorate, the Military Intelligence (MI), during the 1948 India-Pakistan War due to the lack of coordination among the three armed services. Given the political turmoil between 1948 and 1958, the ISI did not really gain prominence until the first military coup in 1958, which brought to power Gen. Ayub Khan. He ruled the country for more than a decade with the ISI as a key instrument of his regime. Put differently, even before it was able to fulfill its original mandate (foreign intelligence), the ISI was sucked into the vortex of Pakistan's turbulent domestic political landscape.

During this time period, the ISI became heavily involved in internal politics to sustain the president's regime and the military's dominance over the state even after Ayub Khan — who assumed the rank of field marshal — stepped down as military chief to consolidate himself as president. This could, to a great degree, help explain the ISI's dismal performance during the 1965 India-Pakistan war. Nonetheless, it was during the Ayub Khan years that the ISI established its primacy over the MI and the civilian Intelligence Bureau (IB).

By the time Ayub Khan was forced out of office in 1969 and army chief Gen. Yahya Khan took over, the ISI had its hands full with domestic political upheaval, as opposed to external threats. After the victory of the East Pakistan-based Awami League (AL) in the 1970 elections and Yahya Khan's refusal to hand power to AL leader Sheikh Mujibur Rahman, civil war broke out between the western and eastern sides of the country, and the ISI was engaged in trying to crush the Bengali rising.

India's intervention in the civil war led to Pakistan's defeat in what has come to be known as the 1971 war. In the aftermath of the war, the country's first democratic leader, President (later Prime Minister) Zulfikar Ali Bhutto, tried to rein in the ISI by appointing Lt. Gen. Ghulam Jilani Khan as its head. Jilani Khan led the directorate for seven years. But even Bhutto increased the agency's domestic role, especially regarding the operation to put down the Baluch insurgency in 1974.

Cold War and Islamism

Another coup in 1977 that ousted Bhutto and brought to power pro-Islamist army chief Gen. Mohammed Zia-ul-Haq, along with Soviet intervention in Afghanistan in 1979, led to the ISI's long relationship with militant Islamist actors. For the next decade, the ISI — first under Gen. Akhtar Abdur Rahman (1980-87) and then Lt. Gen. Hamid Gul (1987-89) — with the help of the CIA and the Saudi General Intelligence Presidency (GIP) backed Islamist fighters to combat Soviet troops supporting the communist People's Democratic Party of Afghanistan (PDPA) government in Kabul. It was under the leadership of Abdur Rahman and Gul that Islamism crept into the body of the ISI.

The war against the Soviets was the culmination of the ISI's attempts to defeat ethnonationalism among the Pashtuns living on both sides of the Durand Line by supporting Islamism as a rival ideology. Thus, the ISI defeated left-wing secular Pashtun nationalism but in the process helped the rise of militant Islamism which, combined with the conservative tribal Pashtun culture, emerged as a much more formidable challenge.

As the Soviet army was pulling out of Afghanistan, al Qaeda's roots were being planted by Arab fighters who had participated in the war against the Soviets. Osama bin Laden and his legion of fighters had developed a close relationship with the ISI during the years when the ISI, CIA and GIP were focused on sustaining a proxy force that could counter the Soviets. But the ISI was more interested in the Afghan groups — specifically the Hizb-i-Islami of Gulbuddin Hekmatyar — because it wanted to see the pro-Soviet Mohammad Najibullah regime ousted and replaced with an Islamabad-friendly government, which would provide Pakistan with "strategic depth" vis-a-vis India.

The hopes of the ISI (at this time led by its overtly pro-jihadist chief Gul) to install a pro-Pakistani government in Kabul were dashed by the intra-Islamist civil war that broke out after the fall of the PDPA government. However, an indigenous rising had been taking shape in Indian-administered Kashmir since 1989, and the ISI used the resources it had developed during the Afghan war to begin aiding these groups and cultivating Kashmir-specific Islamist militant groups.

In the wake of the U.S. State Department's 1992 move to place Pakistan on its watch list of countries suspected of exporting terrorism, the Pakistanis tried to overhaul the ISI in order to avoid additional sanctioning. Lt. Gen. Javed Ashraf Qazi was appointed director-general of the ISI, and during his time (1993-1995) he took significant steps to restructure the organization, trying to move it away from its role of backing Islamists. Qazi introduced new guidelines and replaced quite a few people, but his efforts did not make much of a difference.

One of the reasons was that, while there was a genuine attempt to overhaul the ISI as a body, the directorate was still trying to establish a foothold for Islamabad in Kabul. The ISI achieved its goal of a pro-Pakistani government when it facilitated the rise of a new Pashtun Islamist movement called the Taliban, which had emerged out of the chaos of the early 1990s. Elements within the ISI also facilitated the return of Osama bin Laden and the al Qaeda leadership to Afghanistan in 1996, shortly after the Taliban seized the Afghan capital and bin Laden was forced to leave Sudan.

From the late 1980s onward, the ISI was also heavily involved on the home front, where it played a prominent role in the army's bid to check the power of the four civilian governments that ruled the country between 1988 and 1999. Meanwhile, the ISI and the Pakistani army had been working to send Islamist militants into Indian Kashmir, a process that led to the short Kargil War in the summer of 1999 — the same year in which army chief Gen. Pervez Musharraf, a key figure in Pakistan's Kashmiri Islamist militant project, came to power in an October coup. Despite the reversal the Pakistanis faced in the Kargil War, the Taliban government in Kabul and its ability to continue backing Islamist militants in Kashmir kept the Pakistanis in a comfortable spot, with the Islamist militant proxies firmly under the ISI's control.

9/11 and its Aftermath

The events of Sept. 11, 2001, were a watershed in terms of forcing a behavioral change in the Pakistani state. The Musharraf government went from being an open supporter of the Taliban to (reluctantly) joining the United States in its war against al Qaeda and its host Taliban government. This is where the Pakistani state — especially the ISI — began losing control over the militants it had cultivated for more than a generation.

While there are those within the ISI who see the militants as valuable tools of the state's foreign policy objectives, there are many others who "went native" and developed sympathies for these Islamist militants, even adopting the Islamist ideology of the people who were supposed to be their tools. The Pakistani military-intelligence complex was caught between the need to support the U.S. war against the jihadists and the need to cope with the rise of a hostile government in Afghanistan.

On one hand, the ISI was helping Washington capture and kill al Qaeda members; on the other, it was trying to maintain as much control as possible over the Taliban and other Islamist groups, which were enraged with Islamabad's decision to assist Washington. The ISI hoped its Kashmir operations would not be affected by the war against Islamist militants, but attacks on the Indian parliament in December 2001 brought pressure from New Delhi. Musharraf was forced to ban many Kashmiri groups, which were subsequently allowed to reinvent themselves under different names.

Pakistan and India did step back from the brink of nuclear war in 2002, but the ISI lost control of many Kashmiri Islamist actors because of Musharraf's decision to halt operations in Kashmir. By that time, a trend had emerged in which several disgruntled Islamist actors left the Pakistani orbit and began aligning with al Qaeda, but many were still firmly under the control of the ISI, and others were in between.

As the Islamist militant universe was in flux, so was the ISI. The Pakistani government did make changes to the leadership of the organization, especially after the attempts on Musharraf's life in December 2003. Nevertheless, it is very difficult to steer a whole organization with considerable power and influence in a completely different direction in a short period of time. While the directorate's leadership was busy trying to adjust to the post-9/11 operating environment, others within the middle and junior ranks continued with business as usual.

The next major blow to the ISI's control over the jihadists came when Musharraf — again under pressure from the United States — sent troops into the tribal belt, particularly the Waziristan region, in the spring of 2004. This move created problems for Pakistan's efforts to maintain influence over the Taliban, who had begun resurging in Afghanistan. Military operations which killed hundreds, including civilians, created resentment against the state in the area, played a key role in undermining the authority of the tribal elders through whom Islamabad maintained control over the Federally Administered Tribal Areas (FATA), and contributed to the rise of an indigenous Pakistani Taliban movement alongside the original Afghan Taliban movement.

Over the next two years, Pakistan inked at least three separate ill-fated peace agreements with the militants. Meanwhile, the United States had intensified its covert operations in FATA in the hunt for al Qaeda and Taliban militants, especially in the form of Predator drone strikes. One such strike against a madrassah killed 82 people, mostly young seminary students.

This proved to be the trigger point for a jihadist insurgency, led by top Pakistani Taliban commander Baitullah Mehsud, that struck against dozens of mostly army, police and intelligence personnel and facilities. Suicide bombers' ability to strike with impunity against highly sensitive installations underscored the degree to which the ISI had lost control. Six months later, Musharraf's regime was overwhelmed with political movement after his decision to sack the country's chief justice. The Red Mosque operation on July 3-11, 2007, was another turning point in that it intensified a nascent jihadist insurgency. Pakistani security forces' act of attacking a mosque that led to the deaths of dozens of civilians (including women and children), who were viewed as demanding that "Islamic" law be implemented in a country which officially is an Islamic republic, gave the jihadists a major impetus to advance their campaign against the state. The raid on the mosque triggered a wave of suicide attacks targeting sensitive military installations, including those belonging to the ISI.

Musharraf's stepping down as army chief on Nov. 28, 2007, and his regime's replacement with a weak (albeit democratically elected) government that came to power in Feb. 18 elections exacerbated the situation. And the state is too incoherent to combat Taliban forces that have taken control of significant chunks of territory in the NWFP. The stakeholders in the new civil-military setup realize the need to overhaul the ISI in order to successfully combat the jihadists at home and deal with mounting international pressure from all sides. But they lack the ability to engage in such a massive undertaking. Lack of public support, the fear of making matters worse and the possibility of losing their hold over the state have tied the hands of both the army and the intelligence leadership.

It is very difficult to make out who within the ISI is aiding Islamist militants of various shades. Given the attacks within the country, some ISI elements are definitely collaborating with the jihadists. It is also likely that some of these elements are pressing ahead with private foreign and policy objectives. And then there is the possibility that within the ISI, the right hand does not know what the left hand is doing.

Other than some sketchy open-source material, information on the structure of the ISI is hard to come by. What is known is that beneath the director-general (who is of lieutenant-general rank) there are six major generals, who are also referred to as director-generals of their respective sub-units. Dozens of brigadiers report to these six two-stars, who in turn work with more than a hundred colonels who run various field/regional offices, along with thousands of junior officers. Though it is an army-dominated military organization, some 40 percent of the ISI's employees are civilians who are either retired from active military service or came through the civil service selection process. There are also many retired employees who continue to work with the directorate as contractors and consultants.

The ISI does have different departments that handle the various issues the service deals with, such as the Afghan and Kashmir cells. In addition to the bureaus involved in counterintelligence, signal intelligence and information technology, the ISI maintains an internal security branch which contains the political wing dealing with domestic political issues. The term "Islami wing," a reference to those elements who are either Islamist or pro-Islamist, has also become popularized in the local discourse.

Where It Goes From Here

The ISI evolved fairly rapidly, through domestic and regional crises and threats, into a much more powerful and dominant force in Pakistan, dealing with foreign intelligence, domestic security threats, military and political issues. Over time, it also took on a life of its own as a center of power in Pakistan — something that succeeding governments or regimes could not necessarily control but tried to manage. Attempts to rein in the ISI's power were met with resistance and mixed success and were put aside as new crises arose.

As the ISI evolved, it became the chief conduit for relations with Islamist militants — in part to mitigate their domestic impact, but more to wield or manipulate them as foreign policy tools. These relations with jihadists, though, at times became the end rather than the means, as the ISI monolith continued along with minimal competent oversight or transparency.

Sometimes ISI/Islamist actions ran counter to state intent (as in the trigger for Kargil, for example) and exacerbated political crises and rivalries among various centers of power. At other times, the relationship was seen as useful (support for the Taliban shored up Pakistan's buffer on its western border) but later detrimental (support for the Taliban after 9/11). But the compartmentalized and opaque relations that had developed over time meant the ISI was not necessarily acting as a single unified entity, and operations and relations could and did contradict government policy and intent — even sometimes the intent of the ISI.

The current U.S.-Pakistani crisis is now shining a spotlight on the problems associated with trying to control an ISI that has, in many ways, taken on a life of its own — reaching into domestic and international politics, running its own operations and apparently blurring the lines between the idea of Islamists as a means to an end and Islamism as an end in itself.

Civilian rule in Pakistan has never taken root, and at the present time even the country's military establishment is having a hard time dealing with a rapidly deteriorating crisis of governance. That said, the military remains the only institution with the power to create change — but it can only do so if the country's intelligence system is overhauled. Even though it started out as a reluctant ally of Washington in the U.S.-jihadist war, Pakistan is now locked in its own existential struggle against religious extremism and terrorism, a struggle which simply cannot be won without an intelligence service free of jihadist links.

In the here and now, the ISI has lost control, which is what is needed for the Pakistani state to re-establish its waning writ. The state cannot do this without the help of a robust intelligence agency. Among systemic inertia, the size of the directorate and the fear of losing control over the state and/or national interest, the military's top brass are unable or unwilling to engage in a drastic overhaul of the organization.

The Pakistani state is facing unprecedented internal political and security threats to its integrity which, if not mitigated soon, could lead to its implosion. Under these conditions, cleaning up an intelligence agency as powerful as the ISI can become a very messy affair, to say the least. That said, the Pakistanis cannot hope to regain control of their security situation and address international concerns unless they solve the problems plaguing the ISI.



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