The Australian president of the International Commission of Jurists is calling for the Indonesian Government to hold an inquiry into the massacre on the West Papuan island of Biak 15 years ago.
In July 1998, Indonesian soldiers launched a dawn attack on Papuans who had staged a peaceful demonstration, calling for independence.
The University of Sydney's Centre for Peace and Conflict Studies hosted a citizens' tribunal in July and has now released its findings, saying scores of unarmed civilians were killed, buried in mass graves, or dumped at sea.
It also found people were beaten, tortured, arbitrarily detained and sexually abused.
The tribunal's presiding jurist, John Dowd, says the Indonesian Government should hold an independent judicial inquiry.
"There has clearly been a policy of cover up and cover up does not help anybody including the Indonesian military. We want them to know that this sort of conduct cannot occur in the future and that's why we want proper penalties, proper hearings, to see that justice is done."
John Dowd says the people responsible for the massacre should face criminal proceedings.