The security forces had launched a search operation on a tip-off about the presence of the extremists in Borjhora village, under Lakhipur police station, and cordoned off the area.
On coming face to face with the security team around 11 pm last night, the ultras opened fire and in the retaliatory shooting the two were killed.
A 7.26 mm pistol with 11 rounds of ammunition were recovered from the slain militants, who are yet to be identified.
GNLA is an insurgent outfit based in Meghalaya's Garo Hills region adjacent to Goalpara district.
