Papuan news outlet Tabloid Jubi reports the bodies were found on Thursday in a village in Nduga regency, where violence has flared since last year.
A youth leader from the regency, Samuel Tabuni, is quoted as saying the victims, two of whom were teenagers, were shot by Indonesia's military.
Military spokesperson, Eko Daryanto, told Tabloid Jubi he had not received a report of the shooting.
Meanwhile, Indonesia's President Joko Widodo said the government would review Papua's special autonomy laws to improve conditions for Papuans, the state-news agency Antara reported.
That comes after a request from Papuan leaders who met with the president in Jakarta last month.