Acting on a tip off about the presence of the rebels, specially trained commandos of the state police and CRPF's CoBRA raided Koksi Nengsat village, 32 kilometres from the district headquarters.
On entering the village, the security forces were fired upon, forcing them to retaliate. Two unidentified GNLA militants were shot dead, top police officials told PTI.
The encounter took place at around 6 AM.
A huge cache of arms and ammunition besides detonators, gelatin sticks and communication sets were recovered from the spot, police said.
A combing operation is on in the area to nab the remaining rebels.
The GNLA is an outlawed organisation active in at least five Garo Hills districts.