On a tip off, police waylaid the militants riding on a motorcycle at Sesapani under Dudhnoi police station and asked them to halt, Additional Superintendent of Police Rosy Kalita said.
The extremists of the neighbouring Meghalaya based outfit attempted to flee by firing at the security men, who retaliated killing the three on the spot, Kalita said.
A pistol, some live ammunition and extortion demand letters were recovered from the slain ultras, she said.