CAREFLIGHT line pilot Peter Marris was hoping to catch a glimpse of a life jacket or a bright shirt as he scanned the ocean for two missing Bundaberg fishermen.

Mr Marris was flying one of two helicopters involved in the rescue effort over waters off Fraser Island.

UPDATE | Fishermen's chance of survival 'has expired'

His RACQ CareFlight chopper was tasked early Monday morning and continued trying on Tuesday to locate the men.

Fishermen David Chivers and Matt Roberts were working on the Cassandra before it was found capsized about five nautical miles off Waddy Point on the eastern side of Fraser Island early Monday.

The 18-year veteran said the weather seemed to be better yesterday than on Monday.

"But the wind is quite strong. 25 to 30 knots from the south east," Mr Marris said.

He said the swells were still 2m with lots of white caps and too dangerous for search vessels.

"It's quite rough and not very pleasant for any sea vessels in the search area," Mr Marris said.

Both aircraft are manned with three to four crew per trip which includes a doctor, paramedic, aircrew and a pilot.

"We search at a fairly slow speed from a helicopter at about 200ft," he said.

"With four sets of eyes looking we are just looking for something in the water, anything that is unusual.

"If someone was in a life jacket or wearing bright-coloured clothing and they were on the surface there is a reasonably good chance we would find them."

Mr Marris said the crew would search only with their eyes and if they needed to investigate something they see they would go close to the water to inspect.