A TRAWLER deckhand who planned to gun down a man acquitted of murdering a fisherman and his 10-year-old son has been found dead in a Weipa toilet.

Detectives, including officers from the Homicide Squad in Brisbane, have not ruled out foul play in the death of Brian Edward Dunnett, a crew member of fishing boat El Dorado.

A man discovered Mr Dunnett’s body in a toilet block at Evans Landing about 6am on Saturday, sparking a major investigation.

An autopsy scheduled for tomorrow is expected to shed further light on Mr Dunnett's death.

"We are treating his death as suspicious until we can establish otherwise," Far Northern acting Det Insp Brad Eaton said.

"He was located in the toilet block with significant injuries."

The El Dorado was owned by Bevin Simmonds, who was last seen setting out to check shark nets with son Brad, 10, off Pormpuraaw on June 5, 2003.

An extensive sea, air and land search failed to find any trace of the pair or their boat.

Police charged Michael Gater and his mother Joan with double murder but they were found not guilty in October, 2005.

In January last year, Mr Dunnett, who was called to give evidence but was aboard a fishing boat at the time of the trial, was arrested in Cairns after he was caught carrying a bullet in his jeans.

He was charged with stalking and making violent threats after he told police he would use the .22 round to ""hunt down and kill Michael Gater with it".

Mr Dunnett was fined $500 for possessing the bullet and causing a public nuisance.

Outside court at the time, he told The Cairns Post he was kept awake at night thinking about his friend Mr Simmonds and his son, whose bodies have never been found.

Acting Det Insp Eaton confirmed Mr Dunnett had been working aboard the El Dorado before his death.

"He was well-known in the Gulf community," he said.

He said detectives had interviewed the fishing trawler's crew and other witnesses.

"We're conducting inquiries into the last known movements of the deceased person," acting Det Insp Eaton said.

Forensic officers on Saturday morning combed the toilet block for further clues.