The encounter took place when police raided a GNLA hideout.
"We had specific information about the presence of GNLA cadres in the area and a police team attacked the hide-out. The two civilians were hit in the legs as they ran into the line of fire in panic. The militants, however, managed to escape in the confusion," district superintendent of police Jerry Marak said.
The injured have been identified as Brijil M Sangma (13) and Lakshish Sangma (15). Both were hit on their legs and have been rushed to Goalpara for treatment where their condition was stated to be out of danger.
The suspected GNLA militants were allegedly led by one Rangdat and numbered about five when the police team attacked the hide-out, the SP added.