The chief of Jammu and Kashmir's Al-Qaeda affiliate, Zakir Musa, fled from security forces on Friday night with help of local stone-pelters.
Reports said that the villagers poured out of their homes and pelted stones after security forces cordoned off the village of Zakir Musa.
The clashes erupted as the security forces began conducting house-to-house searches in Noorpora village of Pulwama district.
Police said more security personnel – including the police, the army and the Central Reserve Police Force – had been rushed to the area and three more villages were brought under the extended cordon.
There were unconfirmed reports that Zakir Musa, a former Hizbul Mujahideen commander, could be in the area. But there was no official word on him.
Zakir Musa broke off from Hizbul after declaring that the militancy in Kashmir was to set up a Caliphate.