There are grave fears for a trawler captain last seen in the wheelhouse of his vessel before it capsized off Fraser Island.

Two other crew members were rescued just before 3am on Tuesday about 5km off the island’s east coast.

The pair managed to set off distress flares and were spotted by another commercial fishing boat that was in the area.

The rescued men weren’t hurt and remain aboard the boat that picked them up.

That boat is part of an extensive air and sea search, focused on an area offshore from Indian Head.

The Australian Maritime Safety Authority is co-ordinating the search and says it’s possible the vessel hit an obstruction, causing it to roll.

“The capsized vessel isn’t moving so it may be that it’s connected fast to an obstruction on the sea floor,” a spokesman told AAP.