The army was conducting a search operation at Khouphum Chingthak area in Tamenglong district when the suspected militants fired at them at around 3.30 am.
The army returned fire and in the ensuing encounter, a militant and a civilian were killed, a police officer said.
The civilian, identified as 50-year-old A Rongmei, was killed in the crossfire, the officer said.
Two days back, a security personnel was injured when suspected militants fired at a police party deployed for the visit of Deputy Chief Minister Gaikhangam in Tamenglong district.