Taming the ISI: Implications for Pakistan’s Stability and the War on Terrorism

Publication: Terrorism Monitor Volume: 6 Issue: 20

Inter-Services Intelligence (ISI) is Pakistan’s premier intelligence agency. As such, it has found itself at the center of a dispute between Pakistan and the United States over the prosecution of the War on Terrorism, a dispute fuelled by the two nations’ varying strategic aims. Established just a year after the country’s independence in 1947, the ISI has grown immensely in size, activity and influence over the years. The concept of the ISI being a truly “joint” or “inter-services” organization is a falsehood, since this organization has been always dominated by the Pakistan Army, with barely a smattering of involvement from the other two military services. Moreover, its Director General is always a serving Lieutenant General of the Pakistan Army, answerable only to the Chief of the Army Staff and not to the civilian government, the Ministry of Defense or the Joint Staff Headquarters. [1] By this reckoning, the ISI is essentially an extension of the Directorate General Military Intelligence (DGMI) at the General Headquarters (GHQ), rather than a tri-service national-level institution.

The excessive involvement of the Pakistan Army in the affairs of state has led the ISI to focus on internal/domestic intelligence gathering. While this internal emphasis of the ISI has its roots in the Ayub Khan era (1958-69), its external activities got a significant boost during the Soviet occupation of Afghanistan (1979-1989), when the ISI was put in charge of managing the Afghan mujahideen and their fight against the Soviet invaders, with the active backing of the United States and the financial support of Saudi Arabia.

The links of the ISI with the Islamic militants who routed the Soviet Union from Afghanistan have remained intact ever since and became a major bone of contention between the United States and Pakistan after the U.S.-led invasion of Afghanistan. Many U.S. military and government officials have voiced their concern over ISI’s links with the Taliban, and some have even blamed the ISI for sabotaging U.S. efforts in Afghanistan. The American press has charged that the ISI has used the privileged information it has about American attacks against the Afghan Taliban to forewarn the latter. In fact, the American government believes that a recent suicide-bombing at the Indian embassy in Kabul was carried out by the ISI. In India, the case is even worse: the ISI is blamed for anything violent that happens inside India that the Indian government cannot otherwise explain (Daily Times, September 17).

This backdrop precipitated three significant events: firstly, visits by high-level U.S. intelligence officials on July 12 to meet the new Pakistani leadership and apprise it of the evidence linking the ISI to the Taliban; secondly, the abortive July 26 attempt by the elected government of Prime Minister Yusuf Raza Gillani to place the ISI under the Ministry of Interior; and thirdly, U.S. Assistant Secretary of State Richard Boucher’s statement during an interview on September 17 that the Pakistan Government needed to seriously rein in the ISI and curtail its sphere of activities (The News [Islamabad], September 18).

U.S. Evidence of ISI’s Links with the Taliban

Stephen R. Kappes, the Deputy Director of the Central Intelligence Agency (CIA) accompanied Admiral Michael Mullen, the Chairman of the U.S. Joint Chiefs of Staff on a secret visit to Islamabad on July12. This visit was aimed at confronting Pakistan’s most senior officials with new information about ties between the ISI and militants operating in Pakistan’s tribal areas. The trip was a follow-up to a previous secret visit to Pakistan in January, during which U.S. Intelligence officials sought to press former President Pervez Musharraf to allow the CIA greater latitude to operate in the tribal territories. According to one senior U.S. official, Mr. Kappes delivered a very pointed message, declaring that “Look, we know there’s a connection, not just with Haqqani but also with other bad guys and ISI, and we think you could do more and we want you to do more about it” (New York Times, July 30).

During Prime Minister Gillani’s visit to the United States he was reportedly provided with incontrovertible evidence of the ISI’s continuing links with religious-extremist elements. The Prime Minister, on his return to Pakistan, blithely denied there was a significant problem. Reportedly, PM Gillani had an exclusive meeting with the CIA Director where he was briefed by the latter regarding ISI’s continuing links with the Taliban and was provided with a U.S. “charge-sheet” against the ISI (Dawn [Karachi], September 17).

Gillani’s Decision to Shift Control of ISI

In a move aimed at appeasing the United States while simultaneously projecting its own control and influence, Prime Minister Gillani’s government issued instructions on July 26 for control of the ISI to be shifted to the Ministry of Interior, currently headed by Zardari’s trusted aide Rehman Malik. The timing of the decision was significant, coming on the eve of PM Gillani’s visit to the United States and just two weeks after the secret visit of Mr Kappes to Pakistan (The News, August 5).

As expected, the decision to place the ISI under the Ministry of Interior had to be withdrawn almost immediately under pressure from the powerful Pakistan Army. In retrospect, this decision served no other purpose than to re-establish the limits of power of the democratic government in Islamabad vis-a-vis the Pakistani military.

While there is no doubt that some Pakistanis detest the ISI’s political shenanigans, it is also true that most realize the good that the agency has done for the country in the domain of warding off threats to Pakistan’s national security. Given the current climate where the United States is increasingly perceived as following a policy aimed at downsizing Pakistan geographically and militarily in favor of strengthening India and securing the Central Asian theatre, it is not surprising that the ISI has started being viewed as “Pakistan’s first line of defense” (The News, August 5).

Richard Boucher’s Statement on ISI Reform

Expressing his dissatisfaction at the lack of control exercised by the Pakistan government over the ISI, Deputy Secretary of State Boucher stressed the imperative of reforming the ISI at a private luncheon in Washington, saying “It has to be done” (Dawn, September 17). It might be possible that Gillani made some commitment regarding reining in the ISI during his meetings with Bush administration officials that he was unable to implement on his return, precipitating the outburst from Richard Boucher. Diplomatic sources have indicated that the United States is trying to work out an arrangement with Pakistan for curtailing ISI’s power. Under this new arrangement, the ISI wing which deals with internal security is to be transferred to the Interior Ministry and the agency is to be asked to reduce its role in the war on terror.

The U.S. reckons that such an arrangement would be acceptable to the new civilian government in Islamabad because it can end the agency’s interference in Pakistan’s domestic politics and thus prevent future military takeovers. Taking away the agency’s authority to deal with the militants could help the United States meet its goal of severing the ISI’s alleged links to the Taliban and al-Qaeda.

When the proposal was first discussed with Pakistan’s civilian government, they were not sure they could accomplish this task since they felt that the civilians were still too weak to take on the ISI. Boucher’s statements indicate that the Americans believe that Asif Ali Zardari’s victory in the September presidential elections has created a civilian regime in Islamabad with all the powers it needs to reform the ISI (Dawn, September 17). In the hostile environment that exists in Pakistan today as a result of U.S. cross-border raids into Pakistan and the conduct of the war in Afghanistan, any American policy overture and declaration is bound to be viewed with immense suspicion, and the calls to de-fang the ISI are no exception. With anti-Americanism on the rise, any person or institution targeted by the United States automatically becomes popular and gains favor with the masses. While not all Pakistanis are enamored with the ISI, most view its performance on the external front favorably. To some extent, this is evident even in the Federally Administered Tribal Areas (FATA), where in reaction to U.S. cross-border violations a tribal jirga in Miranshah declared that they would fight alongside the Pakistan Army against any intruders and threatened to attack Afghanistan if the violations did not stop. In the same vein, the extremist militants hiding in FATA have gained greater sympathy and support from the local tribesmen just because they are actively opposing the U.S. and Coalition forces in Afghanistan.

Implications for Pakistan’s Stability

Beset as it is with enormous internal challenges ranging from soaring inflation to extreme insecurity to crippling energy shortages, the Zardari – Gillani government truly finds itself in a bind. While the U.S. administration might incorrectly assume that the civilian government is now in a strong enough position to take on the Army by attempting to transform the ISI, the truth is that the ever-present danger of yet another military take-over is precisely what must be giving Zardari and Gillani sleepless nights. Given that the United States would like to ensure the stability of the newly established democratic order in Islamabad, pitting the Zardari – Gillani regime against the powerful Pakistan Army at this stage could well amount to tolling its death bell. Many believe the ISI is indeed more powerful than the people sitting in cabinet or holding other offices of power. Additionally, there is doubt over whom, if anyone at all, controls this entity (The News, Sept.18). Having a military person at the helm of affairs in former President Musharraf was precisely what was keeping the Pakistan Army quiet and satisfied. With his departure from the scene, the Army returned to viewing the political set-up with utmost wariness and would not hesitate to intervene whenever it perceives that the vital national interests of Pakistan are being compromised by the civilian government.

Impact on the War on Terrorism

From the Pakistani perspective, supporting the Taliban stemmed from the country’s security imperative of “strategic depth,” predicated on having a friendly regime on the north-western frontier. President Musharraf’s decision to withdraw all support for the Taliban and support the U.S. invasion of Afghanistan created a quandary that left the ISI stuck in the middle – it could neither go against what Musharraf wanted nor could it allow its influence and linkage with the Taliban to be completely broken. As such, a dichotomy crept up into Pakistan’s posture towards Afghanistan in general and its support for the U.S.-led war on terrorism in particular. It is highly probable that Musharraf went along with this duplicitous policy of simultaneously supporting the United States without compromising the ISI’s links with the Taliban.

Despite its help in fighting al-Qaeda, the ISI is viewed with deep suspicion by U.S. officials who believe that it retains links to the Taliban and other militants blamed for supporting attacks on U.S. forces. While it is true to state that the ISI has strong links with the Taliban, it is equally important to understand that the maintenance of those links is perceived by most in Pakistan to be an insurance against the possibility of an anti-Islamabad and pro-India Afghanistan. While eliminating the menace of religious extremism and militancy from FATA is definitely construed by Pakistan to be in its national interest, the possibility of an unfriendly Northern Alliance-dominated and pro-Indian regime in Kabul is certainly not in line with Pakistan’s national aims and objectives. From the Pakistani perspective, the war in Afghanistan must end with a favorable and supportive regime in power in Kabul, even if this is made up of the Taliban. From the U.S. point of view, the possibility of the Taliban being allowed to come into power is not considered. It is against this backdrop that one must view the involvement of the ISI with the Taliban – not as abetting terrorism but as protecting Pakistan’s national interest.

An approach based on separating al-Qaeda from the Taliban might allow the U.S. and Pakistan to work together to achieve their respective aims. Currently, the threat faced in Afghanistan is two-fold: the one posed by the international jihadis of al-Qaeda and the other from the local Taliban. While the former is the focus of U.S. and Coalition forces, the latter is the primary threat with which the Afghanistan and Pakistan governments must contend. Whereas the former is threatening virtually the entire world with acts of terrorism, the latter is essentially a liberation struggle against a foreign invasion of Afghanistan. In order to win in this campaign, it is vital that a rift be driven between al-Qaeda and the Taliban. In the implementation of this strategy, the ISI can play a significant role, not only because of its links with the Haqqani group but also its ties with Islamist warlord Gulbuddin Hekmatyar.

In a significant development, the latest shuffle at the senior level of the Pakistan Army saw Lieutenant General Nadeem Taj, the ISI Director General, being replaced after merely a year in office by Lieutenant General Ahmed Shuja Pasha. While some construe this as an attempt to remove known Musharraf loyalists from power, others contend that this could well be an attempt to harmonize the efforts of the military and the ISI in fighting terrorism, since the new DG ISI oversaw the conduct of all military operations against terrorist elements in FATA in his previous assignment as Director General Military Operations at GHQ (Dawn, Sept. 30).


Notwithstanding the imperative of curtailing of its involvement in Pakistan’s domestic situation, the ISI’s external role needs to be maintained, and its links with the Taliban need to be exploited by the United States and Pakistan to their own respective advantage. To avoid the possibility of setting Pakistan’s democratic development back at least a decade, it is vital that any strategy implemented must be seen to further the interests of both allies rather than being perceived as being detrimental to the interests of either. The appointment of Lieutenant General Ahmed Shuja Pasha as the DG ISI is a significant step in the direction of harmonizing the military and intelligence components of the War on Terrorism and could be a major step in removing U.S. apprehensions regarding the ISI.


1. The only exception to this rule was the appointment during the late Benazir Bhutto’s tenure as Prime Minister of Lieutenant General (Retired) Shamsur Rehman Kallu, which was very short-lived and has never been repeated.