The carcass of a 5.2-metre (17-foot) adult male was found in the Fitzroy River in central Queensland on Thursday with a single gunshot wound to the head, the environment department said.
Australia sends anyone who tries to enter by boat without a visa to remote processing facilities in Nauru and on Papua New Guinea's Manus Island. Even those subsequently found to be genuine refugees are barred from settling in Australia.
The 39-year-old man, named by his lawyer as Khaled Merhi, was among the four arrested during raids across Sydney last Saturday, which also led to tightened security at all major Australian airports.
Following the incident involving a MV-22 Osprey -- a hybrid helicopter-turboprop with a chequered safety record -- Japan's defence minister asked Washington to temporarily stop flying them in his country.
The 39-year-old man, named by his lawyer as Khaled Merhi, was among the four arrested during raids across Sydney last Saturday, which also led to tightened security at all major Australian airports.