Three army jawans were also injured in the encounter that took place in Lappa village under Tizit sub-division of the district last night.
Police sources in Tizit told PTI that besides the three militants, the driver of an auto-rickshaw the militants were travelling in, also died on the spot with bullet injuries.
The Territorial Army officer killed in the encounter is Major David Manlun of TA Battalion.
The three injured jawans are undergoing treatment at Military Hospital, Jorhat, Assam, a defence spokesperson said here.
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It was initially reported that the Assam Rifles (AR) had carried out the operations but subsequently, AR sources clarified that a joint team of TA and 12 Para took part in the encounter with the ultras belonging to (NSCN-K) and ULFA.
Police sources, however, said that they are yet to confirm the affiliation of the militants and that the link between the driver and the ultras is also being verified.
Arms and ammunition, which included one AK-56, two AK Chinese made, two grenade, three IED and 270 rounds of ammunitions, were also recovered from the spot.
The spokesman said further details awaited.