Jaish-e-Mohammed in Disarray After Operation Sindoor, ISI Struggles to Bridge Leadership Rift

Jaish-e-Mohammed faces deepening leadership divisions following Operation Sindoor, mysterious killings of operatives and Masood Azhar’s reduced role, while Pakistan’s ISI struggles to contain internal disputes.

Post Published By: Pradeep Tripathi
Updated : 17 October 2026, 6:09 PM IST
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New Delhi: Jaish-e-Mohammed (JeM) is facing mounting internal turmoil as it struggles to recover from the impact of Operation Sindoor, with divisions among its senior leaders and the deaths of key operatives deepening its leadership crisis.

While its ground cadres are reportedly prepared for operations and waiting at launchpads in Pakistan-occupied Kashmir (PoK), the organisation is grappling with disorder at the top and second levels of its leadership.

An Intelligence Bureau official said Pakistan’s Inter-Services Intelligence (ISI) had taken control of JeM and Lashkar-e-Taiba (LeT), directing their activities alongside those of Hizbul Mujahideen. The agency has instructed the three groups to work together and operate on a common front in Jammu and Kashmir.

“Technically, Masood Azhar, Hafiz Saeed and Syed Salahuddin are the chiefs of JeM, LeT and Hizbul Mujahideen, respectively. However, all decisions are taken by the ISI, and these leaders have to report to the spy agency. The ISI has assigned Brigadier Iqbal and Colonel Owaiz to oversee the operations of the three terror outfits,” the official said.

ISI Struggles to Fill Leadership Vacuum

According to officials, although the cadres have been brought under control, the ISI is struggling to resolve disputes between senior leaders and the second tier of the organisation.

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JeM chief Masood Azhar has stepped back from an active role because of ill health and the loss of close family members during Operation Sindoor in May last year.

“The ISI may have taken complete control, but the agency still cannot fill in the void owing to Azhar’s absence,” the official said.

Azhar has long held considerable influence within JeM and other militant groups. His authority helped keep the organisation united, with lower-ranking leaders reluctant to defy his instructions, the official said. His reduced role has left the outfit without the figure who previously held its leadership together.

Another official said clashes between the current leaders were becoming evident during meetings, with disagreements over responsibilities and control of the organisation.

“Disputes have arisen over delegation of assignments and control of the outfit. While a Brigadier and Colonel are at the helm, these leaders still do not consider them leaders as they are not ideologically inclined towards them, like in the case of Azhar,” the official said.

Mysterious Deaths Fuel Internal Suspicions

JeM has also been hit by a series of killings involving its operatives in recent years. Several victims held important positions, and their deaths have added to uncertainty over the group’s leadership. Since 2020, at least 30 operatives linked to JeM and LeT have been killed by unknown gunmen.

The recent death of Lahore-based JeM operational commander Muhammad Asim has reportedly widened divisions within the organisation. Asim, his wife Huma Asim and their son, Talha Asim, were killed after a heavy trailer rammed into their vehicle from behind.

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Members of JeM and surviving relatives have questioned whether the incident was accidental, with some suspecting an internal hit linked to financial dealings. These allegations remain suspicions, rather than established facts.

Asim was responsible for fundraising and developing international channels to move money for JeM’s operations. Officials said he was also tasked with dealing directly with Hamas on funding matters.

Other prominent operatives whose deaths raised questions include Shahid Latif, identified as the mastermind of the 2016 Pathankot attack, Maulana Salman Azhar and Maulana Raheem Ullah Tariq.

Operation Sindoor Deepens JeM’s Crisis

Questions over the loyalty of JeM’s leadership had already emerged following the unexplained deaths, with some members suspecting internal rivalries and possible targeted killings.

Operation Sindoor further weakened the organisation. Indian armed forces destroyed JeM’s headquarters in Bahawalpur, while several cadres and members of Azhar’s close family were killed.

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Azhar subsequently withdrew from the forefront, leaving the organisation without its central ideological figure at a time when it was already struggling with internal disputes and the loss of experienced operatives.

Officials say the combination of leadership divisions, unexplained deaths and the consequences of Operation Sindoor has left JeM facing a serious organisational challenge, despite efforts by Pakistan’s ISI to bring the militant groups under its control.

Location :  New Delhi

Published :  17 October 2026, 5:37 PM IST

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