Police say one person has died and two people are still missing after a fishing boat with five people on board capsized near Port Lincoln yesterday.

Family raised the alarm about 8:30pm on Monday night when the boat failed to return from a fishing trip, and police found the upturned vessel around 2am this morning near Spilsby Island in Spencer Gulf.

“A short time ago we located a deceased person in the water in the same location,” Superintendent Paul Bahr said on Tuesday morning.

“That person is now currently being conveyed back to Port Lincoln by the State Emergency Service and obviously we will be conducting inquiries on behalf of the coroner in regard to that death.

“At this stage we don’t know who that person is, they’re yet to be identified.”

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Police said two survivors — a 44-year-old man and a 13-year-old boy, both from Torrens Park — were found on a reef nearby and winched to safety, and were being treated for hypothermia in Port Lincoln Hospital.

The pair have told them the boat was swamped by a wave around 4pm yesterday, overturning it and throwing the people onboard into the water.

Police said those on board were a group of family members and close friends.

The search is continuing for the two people still missing.

Police said the boat has been recovered and was being brought to shore by another fishing boat.

Police Water Operations Unit, the local sea rescue squadron, a PolAir helicopter and a Challenger aircraft from Australian Search and Rescue have been deployed in the search.

Superintendent Bahr said the boat left Billy Lights Point at Port Lincoln yesterday morning.

After the alarm was raised, rescuers immediately checked local boat ramps before commencing aerial searches.

“We received no EPIRB activation, no radio distress call, no flares were sighted, and from what the survivors have told us it would be highly unlikely there would have been time to have activated any of that,” Superintendent Bahr said.

The Pacific Explorer, a cruiseliner that has more than 2,400 guests on board, has also been diverted to help, a P&O Cruises spokesperson said.

It left Adelaide last night and was due to arrive in Port Lincoln on Tuesday morning as part of its three-day voyage.

The State Emergency Service are involved in the search.(Supplied: Mark Thomas)

Local fisherman, Greg James, said swells on Monday evening were about 15 knots and “a cross flow of swells” could be dangerous around Spilsby Island.

“You got very deep water becoming very shallow on the northern end of Spilsby where there’s a big sandy spit that runs quite a few metres north of the island,” he told ABC Radio Adelaide.

“My thoughts are certainly with those guys.”

Posted , updated