The Indonesian National Commission on Human Rights says preliminary findings indicate the military committed gross abuses in the province of Papua in 2001 and 2003.
The commission says its launching a legal probe into the incidents at Wasior and Wamena .
According to the head of the commission, the incidents in Wamena took place during raids by the army after alleged Free Papua Movement members broke into an armoury.
Army personnel are alleged to have killed seven people, tortured another 48 and forcibly evacuated seven thousand residents.
In Wasior regency, three were killed and sixteen tortured by police after six officers from the police paramilitary force, the Mobile Brigade, were killed by a group of Papuan rebels.