Three missing fishermen have been found dead after an hours-long search and rescue operation in South Australia.

The bodies of three men aged 64, 67 and 74, all from New South Wales, were recovered from waters off the Beachport boat ramp late Sunday night following an eight-hour search operation.

WATCH THE VIDEO ABOVE: Three missing fishermen found dead in South Australia

Know the news with the 7NEWS app: Download today

The alarm was first raised about 2.30pm when the three men, who were in town on a fishing trip, had not returned to shore.

Police said a search of the area was conducted “immediately” after learning of the missing men, with the assistance of Water Operations, PolAir, SES and other aerial assets such as drones. Local boaties also came to assist search efforts.

Superintendent Trent Cox said none of the men were wearing life jackets when they were found and had ignored warnings from locals about dangerous water conditions.

Police searched into the night for the three missing men. Credit: 7NEWS

“It’s a tragic end to what should have been a pretty standard trip for these gentlemen,” he said.

“We pay our respects to these men and hope their families can get through this.”

Cox said the boat belonged to the son of one of the men, but investigators were still trying to understand what caused the boat to overturn.

He also confirmed a member of the public who raised the alarm with police had also been the person who warned the men not to head out in the dangerous conditions, prompting Cox to urge visitors to listen to advice from locals.

“If the locals are saying don’t go out, then there is probably a very good reason for it,” he said.

Cox said another member of the public in a light plane assisted police in the search, and discovered the boat and body of one of the men washed up on shore.

A police helicopter spotted the bodies of the other two men several hours later.

Cox thanked emergency services and locals who assisted in the search and acknowledged the distress it caused.

“Three deaths is just unthinkable and unimaginable. The other side of this is the impact it has on members of the public ... and emergency responders,” he said.

Police have launched an investigation into the deaths and are appealing to locals not to collect any debris from the beach, as it could form a crucial part of their investigation.