Large scale search continues for fisherman lost at sea off Fraser Island

The search continues 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 after 2.30am this morning 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 said it is possible the vessel hit an obstruction, which caused 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 said.

"When the vessel capsized, the crew were working on a different part of the vessel and they last saw the master in the wheelhouse."

A large search area has been established and efforts will resume tomorrow morning in the hope the skipper managed to get off the stricken trawler.