Sengkan K Sangma, 40, was shot dead late last night in Dajong area while Chongkam alias Sengku, who surrendered to the police, was also shot at around the same time in Nongalbibra area, both under East Garo Hills district.
The duo were shot dead for their acts which is against the policies and rules of the GNLA, a note recovered from the dead bodies read, police said.
Four empty cases of AK series rifles and an empty case of pistol was also recovered.
Sohan Shira, GNLA's self-styled C-in-C said, Chonkam was killed because despite their repeated reminder to those who surrendered along with GNLA arms and ammunitions to the police had failed to repay the costs of procurement of the arms.
The GNLA claimed it received payment from only a few surrenderees and hence they were spared.
The militant outfit had been declared a terrorist outfit in the state in January this year.