Police said two of the rebels were killed in Gagrian village in southern Poonch district late on Sunday.
A civilian was injured in the fighting that erupted when security forces closed in on a hideout.
Another rebel was killed in the northwestern district of Kupwara overnight during an encounter with the Indian army, police said, adding the slain man was a Pakistani.
Indian troops have in recent weeks stepped up anti-separatist operations across the disputed region but have themselves suffered heavy casualties.
Kashmir is claimed by both India and Pakistan, while many people in the region itself would like independence.
More than 39,500 people have died in the unrest, according to official figures.
However, separatists put the toll at between 80,000 and 100,000.