A group of fighters were intercepted by troops on Saturday while trying to enter Indian-administered Kashmir from Pakistani territory at Balnoi in Poonch district, some 240km west of winter capital Jammu, Defence spokesman Lieutenant Colonel B.S. Rathore said.
Four fighters were killed in the operation which was continuing, he said.
Troops also shot dead two fighters in the Mohor area of Udhampur district, 150km north of Jammu, late on Friday, Rathore said.
The scenic Himalayan region of Kashmir is divided between India and Pakistan and claimed in full by both.
New Delhi accuses Pakistan of arming, funding and training Islamic fighters waging an anti-India rebellion in Kashmir since 1989.
Pakistan denies the charge, saying it provides only moral and diplomatic support to an "indigenous" uprising in the Muslim-majority territory.
More than 39,500 people have died since the eruption of the insurgency, according to Indian official figures. Separatists put the toll at between 80,000 and 100,000.