Iran–Pakistan: An Undeclared Intelligence War Comes Out into the Open

Tensions flare: Pakistanis chant slogans at a demonstration to condemn Iranian strikes on their country's territory. Image: Associated Press / Alamy

Recent strikes by Iran and Pakistan on each other’s territory in the region of Baluchistan have raised fears of a wider escalation. While the two countries enjoy a near-unbreakable bilateral relationship and close political ties, there has been an ongoing intelligence war between the two since the Islamic Revolution in Tehran.

The last few days have seen global headlines focused on the tit-for-tat airstrikes between Iran and Pakistan. There has been speculation about an Iranian escalation and a wider Middle Eastern conflict that might suck in the Pakistani military. To be clear, no such scenario is on the cards. Iran and Pakistan are already deescalating, with both sides stating a lack of interest in harming their ‘brotherly ties’. However, a clear violation has been committed by both countries, initiated by Iran, and there is historical bad blood when it comes to the Baluch border, with both sides backing each other’s respective proxies. Friction between the two countries has also been raised by competition for control and influence in Afghanistan, overt Pakistani support for Azerbaijan, and Iran’s recruitment of Shia fighters from Pakistan to fight in the Middle East. While the two have not engaged directly in open conflict in the Middle East, there have been numerous irregular small wars between Iran’s Islamic Revolutionary Guard Corps and Pakistan’s Inter-Services Intelligence (ISI).

The Shah’s Steadying Hand to Support a Young Pakistani State

Long before 1979, the Shah of Iran had been one of Pakistan’s foremost backers against a much larger India. Indeed, the Shah even threatened to attack India if it went beyond its remit when it came to attacking East Pakistan (now Bangladesh) in 1971. The Shah along with Jordan and Syria were the only countries in the Islamic world that helped Pakistan with military hardware, intelligence and logistics. All of this is described in some detail in a lucid account by the Shah’s chief courtier, Assadollah Alam.

Furthermore, Baluchistan, which has seen numerous insurgencies sponsored by India and Afghanistan, was always a sore point for the Shah. Iranian jets and military helicopters used to be based in Pakistan while hunting Baluch and Afghan insurgents on both sides of the Iran–Pakistan border. The Shah also repeatedly batted for Pakistan, convincing Nixon and Kissinger to go all the way in supporting Pakistan against the Indians in the 1971 war. In fact, Kissinger’s first trip to Pakistan was to study the Baluch insurgency and its impact on USPersian Gulf security relations. Both Roham Alvandi’s Nixon, Kissinger and the Shah and Alex Vatanka’s Iran and Pakistan go into some detail about the US influence on the Pakistan–Iran joint strategy for security partnerships to protect the Persian Gulf and South Asia from Soviet designs. Baluchistan was central to the security partnership that had endured since 1947, and the Shah was resolute in protecting a young and inexperienced Pakistani state from implosion, especially after the loss of East Pakistan. However, after the ousting of the Shah by Islamic hardliners in 1979, the ebb and flow between Iran and Pakistan began to change for the worse, with an increasing hostility between the two and the convergence over Baluchistan becoming a divergence.

Tehran’s Export of Its Revolution and Changing Tides

During the early years of the Iranian revolution, the two sides continued to maintain close relations and to cooperate on security issues. Pakistan was pivotal in ending the Iran–Iraq war, with former Iranian President Akbar Hashemi Rafsanjani mentioning in his memoirs that along with Syria, Pakistan played a key role as an arbitrator between Tehran and the Saudi-backed coalition led by Saddam Hussein.

However, ties began to worsen after the Soviets left Afghanistan in 1989, as various proxies in the country began to aim their guns at each other. Iran favoured the Shia-dominated warring parties, while the Saudis and Pakistan backed the Sunnis. Before the emergence of the Taliban, the Iranians had already begun to support Shia groups in Afghanistan and Pakistan to challenge a growing Saudi madrassa movement which had been spawned by the Afghan war.

The 1990s and early 2000s also saw a peak in the power and strength of Saudi-funded groups in Pakistan, culminating in multiple bombings and the targeting of Shia mosques and prominent Shia figures. The Iranian consulate in Peshawar was attacked twice, and a senior diplomat was also kidnapped in the same city in 2009.

A clear violation has been committed by both countries, initiated by Iran, and there is historical bad blood when it comes to the Baluch border, with both sides backing each other’s respective proxies

Of course, the use of proxies was a two-way street, and Tehran allegedly had a hand in attacking the Saudi consulate in Karachi. The Pakistanis had not been comfortable with the Iranian-Indian alliance in Afghanistan, which was seen as a direct attempt to undermine both Baluchistan and the Khyber Pakhtunkhwa province in Pakistan. Iran’s cooperation with India over the port of Chabahar (bypassing Pakistan) is also seen by Pakistan as a threat to its own port of Gwadar.

The use of Pakistani Shia fighters in Syria and Iraq was another red line that  crossed by Iran. This took the competition firmly into the sectarian realm, with the risk that thousands of battle-hardened Shia would return to cause havoc in Pakistan, and has upset the status quo in both Afghanistan and Pakistan. In 2020, Javad Zarif, the then Iranian foreign minister, said that Shia fighters could be used to stabilise Afghanistan and Pakistan. This caused considerable anger in both countries, but showed the Iranian desire to dominate by using proxies to fight local civil wars and to provoke ethnic and sectarian strife. The Saudis have also shown an increasing mistrust of Iranian involvement and influence in domestic Pakistani politics that has bordered on purely sectarian lines. Further evidence of this emerged when one of the former president’s right-hand men confessed to spying on the Pakistani military on behalf of the Iranians, with political cover provided by a party the Saudis had always suspected of being pro-Iranian.

The India Factor and Super Spies

After the US-led invasion of Afghanistan in 2001, the new Afghan Republic also pulled closer to India and Iran when it came to trying to isolate Pakistani influence in Afghanistan. In contrast to the Shah’s time when Iran ensured that India kept out of Baluchistan and Afghanistan, Tehran now welcomed India in both Afghanistan and Baluchistan owing to its desire to weaken the Pakistanis’ grip over Afghanistan.

The case of the Indian spy Kulbhushan Jadhav, captured in Iran by the ISI, has led many in Pakistan to suspect that the Iranians have tolerated Indian spies in sensitive Baluch areas, thereby confirming an Iran–India partnership to trap Pakistan. However, the Indians firmly believed that the ISI had used its own Baluch agents to capture Jadhav deep inside Iranian territory. Indian Prime Minister Narendra Modi has made no secret of his desire to raise the temperature in Baluchistan to test Pakistani defences and nerves.

The popular film Kandahar, released last year, portrays a four-way battle on the Iran–Afghanistan–Pakistan border between Pakistani, Indian, US and Iranian intelligence agencies to solidify gains in the Afghan endgame. The Great Game for control of Central Asia has now morphed into an all-out battle between regional players in Afghanistan, as opposed to the Russians and the British of the 19th century. India has even moved into Kabul and established friendly relations with the Taliban, in stark contrast to its entrenched enmity with the group in the 1990s. Iran and India have both cornered Pakistan by doing a U-turn on their ties with the Taliban, ensuring that the ISI can no longer use the group against them.

Geopolitics Trumps Sectarianism

Notwithstanding the use of significant sectarian elements by both sides in the pursuit of strategic and tactical intelligence wins, this fight is by and large about power and influence, from Baluchistan, Afghanistan and Tajikistan all the way to the Caucasus. Pakistan has closely supported Shia-majority Azerbaijan in its fight against Iranian-backed Armenia. Moreover, Pakistan has had multiple Shia Chiefs of Army Staff and a significant number of Shia generals, and so it is clear that in their military calculus, there is no room for sectarian-influenced decisions. Wajahat S Khan of the Atlantic Council, Pakistan’s foremost defence journalist, also believes that Iran and Pakistan are engaged in extensive geopolitical competition in the region.

Notwithstanding the use of significant sectarian elements by both sides, this fight is by and large about power and influence, from Baluchistan, Afghanistan and Tajikistan all the way to the Caucasus

Similarly, in contrast to an almost war-like situation with the Taliban in the 1990s, Tehran is now heavily embedded in the Taliban’s return to power despite the group’s heavy Sunni tilt, with little or no room for Shia minorities in its leadership. The Iranians began recalibrating their previous animosity towards the Taliban by hosting senior Taliban and Al-Qa’ida leaders who were on the run. A lot of this was done out of necessity in order to balance against the Pakistanis and to widen mistrust between Pakistan and the US during their joint quest for an amicable balance of power in 2021. The killing of the Taliban leader Mullah Mansour in 2016 in a drone strike was viewed with suspicion by the Pakistani military, given that Mansour had just crossed the border from Iran into Pakistan. Pakistan alleged that Iran and the US had colluded in making Pakistan the fall guy once again, when in fact the Taliban were now also being supported fully by Tehran. Gulbuddin Hekmatyar, another former Sunni strongman in Afghanistan who was previously a favourite of Pakistan’s, subsequently fled to Iran and became its ally against the US. Iran and Pakistan both used him against each other, with his presence in Kabul after his return during Ashraf Ghani’s government making him a major asset in the ongoing intelligence war.

Major General Sahibzada Isfandiyar Pataudi (Retired), a former Director General of the ISI, told me:

‘There has been an intelligence failure in Iran that has caused a disproportionate response and a violent lashing out in all directions – particularly so in Pakistan’s case – which has been immature and unnecessary. I would not put a sectarian twist on it, nor would I suggest a Cold War-type situation. I do believe, however, believe that Pakistan’s measured response shows our resolve to deal with any violation of our sovereignty.’

Both countries have already restored their diplomatic channels, and their ambassadors will be returning to each other’s capitals very soon. There will not be a further escalation. However, from Karachi to Baluchistan and all the way to the Caucasus, both are waging a covert war for influence and leverage against each other in the modern-day Great Game.

The views expressed in this Commentary are the author’s, and do not represent those of RUSI or any other institution.

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Kamal Alam

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