Pakistan Army and Terrorist Organizations: A Detailed Report on Alleged Relations

 Pakistan Army and Terrorist Organizations: A Detailed Report on Alleged Relations

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I. Introduction

Pakistan’s security establishment, particularly its powerful military and intelligence services—most notably the Inter-Services Intelligence (ISI)—has often been accused of maintaining links with various terrorist and militant organizations. These allegations have emerged from international reports, intelligence agencies, former diplomats, investigative journalists, and regional powers like India, Afghanistan, and the United States.

While the Pakistan Army has played a significant role in counterterrorism operations within its borders, its selective targeting of terror groups and continued tolerance or support for others raise significant questions. This report explores the nature of the Pakistan Army’s alleged relationship with terrorist organizations and how such relationships have influenced internal stability, foreign policy, and regional geopolitics.

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II. Historical Context of the Relationship

2.1 The 1980s: Afghan Jihad and Strategic Depth Doctrine

Soviet-Afghan War (1979–1989): The Pakistan Army and ISI were central to organizing, training, and arming the Afghan mujahideen, with U.S. and Saudi support.

This gave birth to the “strategic depth” doctrine, aimed at:

Gaining influence over Afghanistan

Preventing Indian dominance on both eastern and western fronts

It also laid the foundation for long-term relationships with Islamist militant groups like:

Hezb-e-Islami

Haqqani Network

Gulbuddin Hekmatyar’s forces

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2.2 The 1990s: Kashmir Insurgency and Pakistan’s Proxy Strategy

The Pakistan Army, through the ISI, supported insurgents in Indian-administered Kashmir, including:

Lashkar-e-Taiba (LeT)

Jaish-e-Mohammed (JeM)

Hizbul Mujahideen

These groups received:

Training in Pakistan-administered Kashmir

Weapons and logistical support

Safe havens in Pakistani territory

The ISI viewed these groups as strategic assets for keeping India under pressure and internationalizing the Kashmir dispute.

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2.3 Post-9/11 Shift and Dual Policy

After 9/11, Pakistan became a front-line ally of the U.S. in the War on Terror.

However, the dual policy emerged:

Counterterrorism efforts against anti-state groups like Tehrik-i-Taliban Pakistan (TTP)

Continued support for Afghan Taliban, Haqqani Network, and Kashmiri groups

The Haqqani Network, responsible for deadly attacks in Afghanistan, was dubbed a “veritable arm of the ISI” by Admiral Mike Mullen, former U.S. Chairman of the Joint Chiefs of Staff (2011).

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III. Key Terrorist Organizations Allegedly Protected or Supported by the Pakistan Army

3.1 Afghan Taliban and Haqqani Network

Support Timeline: 1990s–Present

Evidence:

Taliban leaders like Mullah Omar and Mullah Akhtar Mansour reportedly lived in Quetta and Karachi.

Haqqani leaders moved freely in North Waziristan for years.

2016 drone strike killed Mansour deep in Pakistani territory.

Taliban wounded fighters were treated in Pakistani hospitals.

Strategic Use: Maintain influence in Afghanistan and prevent Indian presence.

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3.2 Lashkar-e-Taiba (LeT)

Founded: 1987, with ISI support

Head: Hafiz Saeed, who lived openly in Lahore despite a $10 million U.S. bounty

Major Attack: 2008 Mumbai attacks, killing 166 civilians

State Shelter:

LeT’s charity wing, Jamaat-ud-Dawa (JuD), operated freely in Pakistan for years

Received land, funding, and police protection for rallies

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3.3 Jaish-e-Mohammed (JeM)

Founded: 2000 by Masood Azhar

Alleged Ties: ISI helped in JeM’s creation after Azhar’s release from Indian custody (1999)

Major Attacks:

2001 Indian Parliament attack

2016 Pathankot airbase attack

2019 Pulwama suicide bombing

Despite bans, JeM’s headquarters in Bahawalpur remained functional for years.

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3.4 Hizbul Mujahideen

Backed by: ISI since the 1990s

Focus: Kashmir insurgency

Leader: Syed Salahuddin, listed as a global terrorist by the U.S. in 2017, lived in Pakistan

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3.5 Anti-Shia Militants (Sipah-e-Sahaba and LeJ)

Often tolerated or ignored by the military

Accused of helping the army maintain control in regions with Shia resistance

Leadership arrested under pressure, but released or operated with impunity

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IV. Mechanisms of Protection and Patronage

4.1 Intelligence and Operational Support

ISI has been accused of:

Coordinating training camps

Passing strategic intelligence

Planning attacks (e.g., 2008 Mumbai attacks, 2019 Pulwama)

4.2 Funding and Logistics

Terrorist groups have received funding from state sources under charity or “strategic policy” labels.

Some reports indicate use of Pakistan’s embassies abroad to move money.

4.3 Legal and Political Immunity

Leaders of LeT, JeM, and JuD often face token arrests but are never prosecuted seriously.

Masood Azhar and Hafiz Saeed enjoyed police escorts and gave public speeches.

Courts often cite “lack of evidence” due to weak prosecution and ISI interference.

4.4 Media and Ideological Shielding

State-controlled media underreports militant activities.

Religious organizations linked to terror groups have been part of mainstream politics (e.g., Milli Muslim League, political wing of JuD).

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V. Geopolitical Motivations Behind the Relationship

5.1 India-Centric Strategic Doctrine

Kashmir remains the core issue driving Pakistan’s strategy.

Militants are viewed as a low-cost asymmetric warfare tool to counter India’s conventional military superiority.

5.2 Afghanistan Policy

Pakistan seeks a friendly (preferably Taliban-led) government in Kabul.

Strategic depth ensures no Indian influence on the western border.

Haqqani Network and Afghan Taliban were essential components of this policy.

5.3 Internal Balancing and Islamization

Militant groups helped Islamize society, aligning with Zia-ul-Haq’s legacy.

Radical clerics and jihadi networks served as ideological buffers against democratic or secular movements.

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VI. International Evidence and Reports

6.1 U.S. Congressional and Pentagon Reports

Multiple U.S. reports accuse Pakistan of harboring terrorists.

Pentagon (2018): “Pakistan continues to provide safe haven to Taliban leadership.”

6.2 FATF (Financial Action Task Force)

Placed Pakistan on its Grey List (2018–2022) due to terror financing.

Demanded prosecution of LeT, JeM, and JuD leadership.

6.3 Wikileaks and Osama bin Laden Files

ISI suspected of sheltering bin Laden, found near a Pakistani military base in Abbottabad (2011).

U.S. intelligence documents reveal regular communication between ISI officers and terror groups.

6.4 Reports by Global Think Tanks

Brookings, Carnegie Endowment, RAND Corporation: All documented Pakistan's selective counterterrorism approach.

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VII. Domestic Backlash and Blowback

Anti-state groups like Tehrik-i-Taliban Pakistan (TTP) emerged as a blowback from earlier jihadist patronage.

Over 80,000 Pakistanis have died in terrorist violence (2001–2023).

Army Public School Massacre (2014) triggered national outrage and forced military to rethink its policy.

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VIII. Shifts and Recent Trends

8.1 Tactical Repression Under International Pressure

Post-2019, Pakistan made symbolic arrests of Hafiz Saeed and Masood Azhar.

FATF pressure led to some terror financing trials.

However, many view these as cosmetic moves to avoid blacklisting.

8.2 Taliban Takeover in Afghanistan (2021)

Seen as a strategic victory for Pakistan, but also emboldened TTP.

Pakistan asked Afghan Taliban to mediate with TTP, but talks failed.

TTP resumed attacks, especially in KP and Balochistan.

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IX. Consequences of the Army-Terrorist Nexus

9.1 For Pakistan

Domestic insecurity and massive economic losses

Loss of global credibility

Risk of civil-military divide deepening

Militancy spilling beyond “controlled boundaries”

9.2 For India and Afghanistan

Constant security threats and cross-border tensions

Difficulty in pursuing peace processes

Border skirmishes and attacks on embassies and military bases

9.3 For Global Security

Pakistan has become a safe haven for global jihadists

Raised concerns about nuclear arsenal security

Attracted sanctions, pressure from U.S., EU, FATF

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X. Conclusion

The relationship between the Pakistan Army and terrorist organizations is one of strategic pragmatism and ideological alignment, cultivated over decades. While the Pakistan Army has suffered at the hands of some militant groups, it has selectively supported others for geopolitical gains.

This duality has earned Pakistan the label of a “state sponsor of terrorism” in international discourse, despite its counterterrorism efforts. As the regional and global context shifts, Pakistan faces increasing pressure to decisively break ties with all terror groups and enforce consistent, transparent, and verifiable counterterrorism measures.

Without such a shift, the cost—both internal and international—will continue to grow.