A former Dutch Colony, West Papua was incorporated into Indonesia in 1963. Channel 4 News has not been able to independently verify the footage, but, recognising the serious nature of the material ministers in Jakarta have ordered a full investigation into the video only weeks before President Barack Obama visits the country.
West Papua borders the independent state of Papua New Guinea, just 250km north of Australia.
This footage emerged on the internet and was filmed in the Puncak Jaya region where troops have been deployed to counter an armed independence movement.
This report by Kylie Morris contains images viewers may find disturbing.