The skipper of a boat that a fisherman was believed to have fallen overboard from yesterday, said he and his 14-year-old son searched the entire vessel before alerting authorities that a crewman was missing off Double Island Point.

Key points: The search cost RACQ LifeFlight organisation a quarter of a million dollars

The search cost RACQ LifeFlight organisation a quarter of a million dollars The missing fisherman was found in a compartment of the boat after missing for 12 hours

The missing fisherman was found in a compartment of the boat after missing for 12 hours The skipper of the boat says he searched the vessel before alerting authorities

Peter Rockliff said he was about to shutdown and take a break when he tasked 45-year-old Steve Gallagher with some final jobs about 2.30am.

Mr Rockcliff said he "looked away for 30 seconds" at his computer, turned back, and Mr Gallagher was nowhere to be seen.

"I woke George up and said 'I think Steve's gone over the side', we searched the boat first and we looked everywhere and couldn't find him," he said.

"So obviously your next thought is 'he's gone overboard'. We turned around and put a mark where we were and went back up the direction we came and then shut the boat engine down so it was all silent.

"We yelled his name out a few times and didn't get a reply, so we call triple zero and told them we thought he'd gone over."

Mr Rockcliff said his initial thoughts were of the worst, having known Mr Gallagher for many years, and how he would tell his family.

"I was devastated. That's every skipper's worst fear to lose someone over the side," he said.

"I was thinking 'what am I going to say to his kids'. He has a boy the same age as George at home."

The fisherman was taken to waiting paramedics by water police. ( ABC News )

Mr Rockcliff said it wasn't until hours into the search that he noticed a handle on a floor compartment had been moved and a small part of a blue shirt sticking out the side.

When he opened it up, he found Mr Gallagher laying beneath a pile of ropes.

"I came up the back to get some ice out of the esky, I saw the handle wasn't how I left it, because I'd already looked down there," he said.

"That's when I opened it up and had a good thorough look and saw him hiding up under the ropes... he was in a bad way.

"I don't know why he didn't respond, he heard us and knew what was going on."

Mr Rockcliff said while he and his son were relieved to find the fisherman, there was also a lot of anger about the wasted time and resources.

"I mean we'd been looking for hours! And the amount of time, money and effort that went into looking for him, the time wasted, I mean there's a lot of anger there, but obviously I'm pleased he's just alive," he said.

"This is the best outcome possible, but yeah especially when I had the young fella out on his first trip with me, this is just the last thing I wanted.

"Everyone involved just did a great job, I can't praise them enough."

Mr Gallagher was brought back to Mooloolaba Port to the water police headquarters around 6:00pm on Wednesday and was transported to Sunshine Coast University Hospital by paramedics.

The hospital confirmed he is still receiving treatment for a "medical condition" but would not elaborate.

Search cost hundreds of thousands of dollars

LifeFlight crew members were looking for the fisherman, who was actually on the boat the whole time. ( Supplied: RACQ LifeFlight )

The RACQ LifeFlight organisation said the search cost the company a quarter of a million dollars before Mr Gallagher was found.

The search efforts included eight helicopters, two fixed-wing aircrafts, one jet, two water police vessels, two fishing vessels and a Coast Guard vessel.

RACQ LifeFlight Rescue spokeswoman Julie Korner estimated her organisation alone spent $250,000 on the search.

"In total we had three RACQ LifeFlight helicopters in the grid pattern looking for this man yesterday," Ms Korner said.

"We would estimate the cost of providing three helicopters with their own medical crews would be in the vicinity of a quarter of a million dollars."

Ms Korner said it was unclear if the organisation would seek compensation for the rescue.

"It is not up to RACQ Lifeflight rescue to make judgement or ever question the validity of a call for help," she said.

"This is very early in this situation, so we will wait and see how it plays out.

"Crews are dedicated to saving and preserving life … when our crews heard that this gentleman had been found safe and well they were relieved to hear that he was OK," she said.

"There had been grave concerns for his safety … so all of the crews were just pleased that there was a positive outcome."

Mooloolaba Voluntary Marine Rescue commander Bill Asher said it was unbelievable the lost man was found on board.

"The cost alone in helicopters and things — you're talking hundreds of thousands of dollars," he said.

"The fact they didn't do an inspection on the boat. We can't believe that you wouldn't first of all check the accommodation on your vessel."

The search area was about 133 square miles offshore from Double Island Point.

Police have confirmed they are no longer investigating the incident.