The Catholic report says Muslims are being radicalised in the once predominantly Christian Papuan provinces, and very active militias are burning down Papuan houses.
The report was compiled by the Brisbane Catholic Justice and Peace Commission's Shadow Human Rights Fact Finding Mission to West Papua, following a visit last month.
It has not yet been publicly released, nor comment sought from Indonesian authorities.
The report documents religious, social and economic discrimination, including the carving up of land for major developments, which benefit multinationals and exclude Papuans.
It refers to a slow-motion genocide and states that the Indonesians want to replace the Christian religion with Islam.
More than 200 community leaders in Jayapura, Merauke, Timika and Sorong were interviewed during the visit.