Ahmad Kamal, spokesman of the Papua Police, confirmed the killings of the civilians.
Bodies of the three civilians were taken to the local police, but information on the two injured residents was not available.
"There is a problem in the communication network, so latest developments in the area are not as yet known," he revealed.
The civilians, who were attacked by the separatists, lived near the Kenyam airport area.
Earlier, on Monday, at 9:30 a.m. local time, a Twin-Otter aircraft owned by Trigana, was shot at and its pilot, Kamil, was injured by bullet shrapnel.
The aircraft, with flight code PK-RYU, carried 18 personnel deployed to secure the upcoming gubernatorial election, or pilkada, to be held simultaneously across Indonesia on June 27, 2018.