The men were on the fishing boat Dianne on their way to harvest sea cucumbers when the vessel overturned near the town of 1770 in rough seas on Monday night.

The wreckage of the 17-metre commercial trawler was found using sonar on Friday afternoon, about two to three nautical miles off Round Hill Headland.

Ruben McDornan survived, after being plucked from rough seas by a passing yacht on Tuesday, and the bodies of two men were recovered on Saturday.

The six fishermen are 45-year-old skipper Ben Leahy and crew members Adam Bidner, 33, Zach Feeney, 28, Adam Hoffman, 30, Chris Sammut, 34, and Eli Tonks, 39.

On Sunday afternoon, police announced they had finished clearing the wreckage of the commerical fishing vessel.

But despite a painstaking and thorough search, which involved clearing a large amount of debris, no further bodies were found inside the boat.

The families of the six crew members were advised of the latest developments.

Inspector Darren Somerville said police still did not know where the remaining four men were, but the operation was in the recovery stage.

He said the bodies of the two men found on Saturday had been identified but not all the next of kin had been contacted, so the families had asked for their names to not be released yet.

Inspector Somerville said the families were upset.

"It doesn't really change that they have lost their loved ones, it just changes that we have been unable to locate the bodies, so I guess they're still very upset," he said.

"A lot of the families will be returning to their homes, I should imagine, over the coming days."

Inspector Somerville said the weather conditions were the best they had been so far for the police divers on Sunday, but they could still only dive for 13 minutes each time due to the depth of the water.

The divers were finished for the day on Sunday and were due to return to Gladstone.

"Unless we find anything extra with our soundings tomorrow, there'll be no more police diving at this stage," Inspector Somerville said.

On Sunday, patrols were conducted with volunteer marine rescue boats and a fixed-wing aircraft that swept the coast from Round Hill to Cape Capricorn, but found nothing of interest related to the vessel.

Police will speak with the coroner and decide in the coming days about what happens with the trawler, but it could be weeks before it is recovered.

At first light on Monday, two police vessels will conduct a further sonar search in the area.

A fixed-wing aircraft will also conduct more sweeps of the coast and there will also be further land-based foot and vehicle patrols.

Police said they were working hard to ensure the families could get some measure of closure.