Israel’s covert war in Balochistan binds Iran and Pakistan in rare alliance

As Israel and India increase their subversion and support of militant Baloch groups on Iran and Pakistan's borders, Tehran and Islamabad deepen security coordination to thwart the foreign-backed separatism.

F.M. Shakil

AUG 16, 2025

https://thecradle.co/articles/israels-covert-war-in-balochistan-binds-iran-and-pakistan-in-rare-alliance

When Iranian President Masoud Pezeshkian visited Pakistan on 2 August for the first time since taking office, the intensifying security threats in the strategic Sistan-and-Balochistan province were top of the agenda.

The urgency was evident in the inclusion of Mansour Bijar, an ethnic Baloch recently appointed governor of the province, in the presidential delegation. The joint declaration at the close of Pezeshkian's two-day visit offered unusually direct language, reaffirming both Iran and Pakistan's resolve to combat militancy along their shared border.

As Mansur Khan Mahsud, executive director of Pakistan's FATA Research Centre (FRC), tells The Cradle:

“It seems that Tehran and Islamabad have finally reached a consensus, conceding that the tensions in Balochistan have transitioned from a localized uprising to a multifaceted geopolitical game. This situation enthralled several regional entities, which then looked to manipulate and exploit the disgruntled factions to achieve their strategic objectives.” 

Tehran targets external meddling

Prior to the fatal helicopter crash on 20 May that killed Pezeshkian’s predecessor president Ebrahim Raisi and his foreign minister Hossein Amir-Abdollahian – senior Iranian officials had publicly acknowledged the role of foreign actors in fomenting unrest inside their borders.

During a joint press conference in Islamabad on 29 January, Amir-Abdollahian noted that “third countries” were aiding militant factions operating in the Iran–Pakistan borderlands. He avoided naming states but insisted that these actors consistently obstruct policies that serve Iranian and Pakistani interests.

On 28 July of this year, Russia's TASS news agency reported that Iran's Intelligence Ministry had thwarted the infiltration of at least 450 foreign fighters during the intense military conflict with Israel in June. Intelligence officials identified 300 operatives near Iran's southeastern border, allegedly preparing for cross-border attacks. During the 12-day war, Iranian police are reported to have arrested around 21,000 people on various charges or for interrogation.

Iranian authorities directly implicated Tel Aviv, accusing the Israelis of recruiting and deploying mercenaries through the Balochistan Liberation United Front (BLUF), a faction believed to unite separatists from both the Iranian and Pakistani Baloch regions.

“During the recent 12-day standoff between Iran and Israel, Tehran noticed a tight-knit connection between Baloch separatists and Israel. Their sharing of intelligence with Tel Aviv led to significant human and infrastructure losses for Iran,” Mahsud explains.

MEMRI's front in Balochistan

The Middle East Media Research Institute (MEMRI), a pro-Israel think tank based in Washington, launched its Balochistan Studies Project (BSP) on 12 June. Iran and Pakistan view this initiative as part of a coordinated Indo-Israeli bid to destabilize the region. According to Abdullah Khan, chairman of the Pakistan Institute for Conflict and Security Studies (PICSS) in Islamabad, a think tank that deals with militancy and terrorism: 

“Iran is enhancing its ties with Pakistan in the background of militants' increased alignment with Israel. Their liaison with Tel Aviv would further crystallize when Iran shifts its policies and takes action against BLA and BLF sanctuaries within its territory. India has cultivated strong ties with both groups, enabling it to serve as a bridge to connect them with Israel.” 

In the days leading up to Pezeshkian's visit, the Islamabad Policy Institute (IPI) think tank convened a roundtable session in the Pakistani capital, emphasizing the need for a stronger partnership to protect mutual interests in a swiftly evolving geopolitical environment, where both countries face common challenges, including those presented by Israel. 
Senator Mushahid Hussain, Pakistan's former information minister and head of the Senate Foreign Affairs and Defence Committees, who attended the seminar, tells The Cradle that the emerging “Indo-Israel axis” acts as a warning for both Iran and Pakistan, highlighting the necessity for a collaborative stance from both countries:

“Pakistan’s support for Iran highlights the lasting connection between the two countries, grounded in common interests and focused on addressing the challenges they both face. Both nations have endured the storm of aggression based on ‘false pretexts’ and have dispelled the illusion of India and Israel's invincibility through their steadfast resilience.” 

Among those enlisted in MEMRI's BSP is Mir Yar Baloch, a Baloch nationalist, scholar, and leading figure in the Free Balochistan Movement (FBM), says Abdullah Khan. Baloch has openly called for an independent secular Balochistan spanning both Iran and Pakistan, and has reportedly sought Indian assistance to realize this project.

Reportedly, the Baloch militancy primarily revolves around two groups: the BLA-Aslam Baloch faction, currently referred to as the BLA Bashir Zeb faction, and the Baloch Liberation Front (BLF), which is led by Dr Allah Nazar.

“The decision to choose someone with limited impact in Balochistan is intriguing, given the fact that the ongoing militancy is directed by middle-class youth leaders who function autonomously from tribal leadership,” Khan explains.

Balochistan: Proxy war zone 

The increasing visibility of Israeli intelligence in Balochistan reveals the extent to which the region has become a theater for hostile proxy activity. 

Iranian and Pakistani officials are deeply concerned about the growing cooperation between Israel's Mossad and these militant Baloch groups – an alliance that has the potential to alter the fundamental foundations of Pakistan and Iran's mineral-rich yet underdeveloped region.

Last week, a Eurasia Review op-ed also reported that the Mossad was deeply embedded in operations targeting Iran's southeastern front. The porous Iran–Pakistan border provides ample opportunity for smuggling, covert infiltration, and cross-border strikes.

A common view in Islamabad is that India, which butted heads with Pakistan in a brief, intense military engagement in May, aims to instigate changes within the country, simultaneously maintaining vigilance against the Chinese Belt and Road Initiative (BRI) that traverses through Balochistan. New Delhi’s own role in Balochistan is well-documented. 

The Research and Analysis Wing (RAW) of India has already established its involvement in the Baloch imbroglio. In 2016, Pakistani forces apprehended Indian naval officer Kulbhushan Jadhav, who confessed to orchestrating sabotage operations and liaising with Baloch insurgents. His arrest, and the evidence Pakistan presented to the UN Security Council, substantiated longstanding claims of India's RAW agency coordinating subversive activity in the province. Mahsud opined:

“The likelihood that Israel has contacts with the Baloch militants is increasing, especially considering the close interaction between India and Israel. Israeli military personnel and Mossad agents were reportedly present in India when it had a 100-hour brawl with Pakistan,”

Iran–Pakistan security reset 

Until recently, Tehran and Islamabad routinely accused each other of sheltering anti-state militants. The tit-for-tat airstrikes both countries launched in early 2024 reflected how deep those frustrations had grown. Yet in the past year, and more so in the past few months, the regional calculus has shifted dramatically.

The urgency is real. It is rare for a day to go by without an attack on a member of Iran's or Pakistan's security personnel, on or within their respective borders. In just the past month, seven commissioned officers of Pakistan's military were killed in militant attacks, the latest on 5 August. These losses do not include lower-ranking soldiers, whose deaths often go unreported.

Iran and Pakistan have since enacted joint intelligence-sharing protocols and counterterrorism mechanisms to better manage their 900-kilometer border, where rugged terrain provides cover for insurgents, smugglers, and traffickers.

The Indo-Israeli campaign to weaponize Baloch separatism has added a dangerous new layer to the region's conflicts. How effectively Iran and Pakistan can repel this effort may define the next chapter in the Baloch insurgency.