A fisherman thought to be missing at sea for more than 12 hours has been found safe and asleep onboard the commercial fishing vessel.

The man was found by members of the crew sleeping in a compartment on the boat just before 4:00pm.

Water Police travelled to the vessel to speak to the man and try to determine the circumstances surrounding the incident.

The man was brought back to shore and then taken in an ambulance from the water police headquarters.

The search efforts were stood down once he was found, which included eight helicopters, two fixed-wing aircrafts, one jet, two water police vessels, two fishing vessels and a Coast Guard vessel.

The man reported missing is a spanner crab fisherman who also has family on the Sunshine Coast and is understood to be an experienced seaman.

Earlier on Wednesday, Sunshine Coast water police said the 45-year-old was last seen about 2:15am by the boat's skipper and it was "not known how he went overboard" but that there were "great fears" held for his safety.

Initial reports suggested the boat was drifting in calm water at the time the man supposedly disappeared.

The fisherman was taken in an ambulance from the water police headquarters in Mooloolaba after he arrived back. ( ABC News: Jacqui Street )

Many questions remain unanswered

The owner of Rockcliff Seafoods, who the vessel is contracted to, said she is extremely relieved to hear that the fisherman is alive and well.

Helen Rockcliff said staff had been on edge all day hoping for a positive result but said many questions are still unanswered.

"We're very happy it's been a positive end to this, it's been an exhausting day for everyone," she said.

"We're still unsure of the circumstance around what's happened but we're sure police will get to the bottom of it.

"We're just relieved that Steve has been found safe."

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

An urgent PAN-PAN radio alert was sent to all boat users across the Sunshine Coast, asking them to keep an eye out for the man.

The skipper of the vessel Barameda-K and his 14-year-old son also took part in the search for the man.

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