A policeman, two militants and a civilian were killed, while three paramilitary personnel injured in a gun battle in Jammu and Kashmir's capital Srinagar.
Local police confirmed the killing of two militants.
The slain civilian, Rayees Ahmad, was identified as the son of the house owner in which local militants were staying.
The joint resistance leadership has given a shutdown call on Thursday.
"In Downtown Srinagar, son of house owner killed in cold blood, owner suffers cardiac arrest, two armed youth martyred, houses razed to ground, journalists and photographers beaten," Mirwaiz Umar, a top resistance leader, wrote on Twitter.
The Indian authorities suspended internet in Srinagar, shutdown the educational institutions and curfew like restrictions were imposed in several areas.
Protests and clashes between people and Indian forces were reported from several areas in Srinagar.
Kashmir, a Muslim-majority Himalayan region, is held by India and Pakistan in parts and claimed by both in full. A small sliver of Kashmir is also held by China.
Since they were partitioned in 1947, the two countries have fought three wars -- in 1948, 1965 and 1971 -- two of them over Kashmir.
Also, in Siachen glacier in northern Kashmir, Indian and Pakistani troops have fought intermittently since 1984. A cease-fire came into effect in 2003.
Some Kashmiri groups in Jammu and Kashmir have been fighting against Indian rule for independence, or for unification with neighboring Pakistan.
According to several human rights organizations, thousands of people have reportedly been killed in the conflict in the region since 1989.
