Analyst Major General (retired) Ashok Mehta said militants were using the mosques as part of an operational strategy.
"Stepped up activity by the militants in proximity to mosques could be an attempt to incite Indian security forces to storm the shrines and, in the process, upset the religious sentiments of the local Muslim population."
Militants seeking shelter in mosques is not a recent phenomenon, Mehta said, noting several such incidents in the past decade.
In May 1995, a two-month siege of Charar-i-Sharif ended with 40 militants escaping. But most of the town surrounding the shrine was heavily damaged in a fire, which both sides accused the other of starting.
In March 1996, 17 militants were killed after they were forced out of the lakeside Hazratbal Mosque in Srinagar.
"Militants think escaping into mosques is the best bet as the chances of security forces storming the shrines are few," Mehta said.
The Indian security forces in Muslim-majority Kashmir are under orders not to take offensive action against militants holed up inside any place of worship.
"You can lay a siege to the place, cut off the water, electricity and food supplies. But offensive action is ruled out," Mehta said.
However, "Each case is dealt with as per the situation on the ground," he added.
The final operation on June 8 to flush out six militants from a mosque in Shangus village, 57 kilometres south of Srinagar, caused some damage to the shrine's annexe.
Subrahmanyam argued that any sacrilege was caused by the militants, not the security forces.
"You cannot commit acts of violence against innocent people and then seek refuge in a religious place in the name of religion," he said.
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