The three militants forcibly took shelter in a villager's house at Mungreng along the Assam-Meghalaya border to make bombs which were to be used to cause disturbance during Independence day, police said.
Two of the those killed were identified as Kandeswar Rabha and Babul Rabha of Paresh Baruah's ULFA(I) faction, they said.
A hand grenade, a pistol with ammunition and documents were recovered from the spot.