A pilot and co-pilot of a small commercial Smartair plane died after assailants opened fire on the aircraft as it landed at Korowai airport in Boven Digoel, South Papua province, on Wednesday morning, police spokesman Cahyo Sukarnito said.
The plane was carrying 13 passengers in addition to the two pilots.
When the shooting began, the pilots and passengers left the plane and fled into a nearby forest, he said.
The pilot and co-pilot were killed but all passengers were unharmed.
Cahyo said it was unclear who carried out the attack when asked on whether Papuan rebel groups were suspected.
Smartair did not respond to a request for comment.
Separately, Indonesia's military said the Free Papua Movement rebel group attacked a convoy of PT Freeport Indonesia, part of US miner Freeport-McMoRan Inc, killing a soldier and injuring another officer and a Freeport employee.
Freeport Indonesia said the attack occurred on Wednesday afternoon on the main road to the mining town of Tembagapura, prompting the temporary closure of access to the area.
The rebel group did not immediately respond to a request for comment.
A low-level but increasingly deadly conflict between security forces and separatists has simmered in resource-rich Papua ever since the region was brought under Indonesian control in a 1969 vote overseen by the United Nations, a process that remains disputed by independence supporters.
