Billy Frost, 29, was found in the water off Amity Point after taking his vessel out about 6am on Tuesday and not returning three hours later as scheduled.

When Mr Frost failed to arrive, a colleague went searching and found the dead skipper and his boat.

Friend Keisha Proghoulis said Mr Frost left behind many close friends.

"I luved [sic] your ability to fill a room with laughter, you leave behind a lot of broken-hearted peeps," she said, on social media.

"I for one will miss our partner in crime sessions ... your time here was not wasted, you touched a lotta peeps and I promise to guide ur bewdiful wife thru this time. [sic]"

Crime-scene police involved in the investigation decided the death fell under the jurisdiction of the Australian Maritime Safety Authority.

AMSA investigators met the boat when it was brought back to the Port of Brisbane on Tuesday, but were in the early stages of their investigation.

It is understood Mr Frost was not attacked by a shark.

Fisheries Minister Mark Furner said his heart went out to the young man's family.

"I expect water police, the coroner, the Australian Marine Safety Authority and Work Safe Queensland will investigate," he said.

A 33-year-old Victorian doctor, Daniel Christidis, died in Cid Harbour in November, and two shark maulings occurred 24 hours apart in September at the same location.

The shark control program came into question when LNP Whitsundays MP Jason Costigan called for drum lines to be immediately installed in Cid Harbour permanently.

However, Tourism Minister Kate Jones said the state government had taken advice from locals, who said they would prefer not to have drum lines and decided to ignore Mr Costigan's request.

- with Felicity Caldwell