Nicholas F. Goselin, an American pilot, was reported killed after his PT AMA aircraft landed in Balinggama village in Yahukimo, with communications lost soon afterward, according to Indonesia's civil aviation authority.
TPNPB separatists said they shot him dead and burned the plane because it allegedly carried Indonesian troops into a zone where the group had banned civilian flights.
Indonesia's military and the U.S. Embassy had not commented, while Papua police said they were still trying to verify the condition of the pilot and seven passengers before sending a team on Friday.
Yahukimo's mountainous terrain, lack of road access and weather dependence have slowed the response and left no immediate information on the seven Indonesians aboard.
The claim follows earlier attacks on foreign pilots in Papua, where a decades-long insurgency has intensified over the past year with dozens of rebels, security personnel and civilians killed.