Tom Allard – The Indonesian military has murdered independence activists, raped women and razed villages in Papua, a report by University of Sydney researchers alleges.

Citing witness accounts and testimony from church groups and other activists, the report, Genocide in West Papua?, has renewed calls for a change in attitude from Australia.

Both the main Australian political parties have told Jakarta they support its sovereignty over Papua.

A former Dutch territory, resource-rich Papua was fully incorporated into Indonesia in 1969 under a highly controversial United Nations-supervised ballot involving only 1025 voters in a region with a population of almost a million at the time.

However, the report says most indigenous Papuans still want independence and that a build-up of Indonesian troops in recent months has been accompanied by new abuses and repression.

"Military operations have led to thousands of deaths in Papua and continue to cost lives," it says.

Kopassus troops – Indonesian special forces – were responsible for the death of a pro-independence priest, the Reverend Elisa Tabuni, last year, the report said, citing the Papuan Baptist Church as its source.

Indonesian troops were also responsible for burning 371 homes in Puncak Jaya and stealing livestock at the end of last year, it said. Soldiers raped at least one woman during the operation, unnamed witnesses said. More than 6000 displaced Papuans were said to remain in hiding in the jungle.

It is also alleged that as recently as February, more property was destroyed in Papuan villages while Jakarta-backed militias had also murdered dissidents.

The report also outlines corrupt Indonesian military activities including illegal logging, rigged construction projects and theft of aid, as well as prostitution and the spread of HIV/AIDS.

A spokeswoman at the Indonesia embassy in Canberra denied the allegations and called on the University of Sydney researchers to hand over evidence so it could investigate.