Authorities launched a second search for the Margrel on Tuesday morning after a man on board, believed to be Tony Higgins, reported it was taking water off Granite Island, south of Adelaide.

Police began a search with a helicopter and fixed-wing aircraft, with volunteers from Sea Rescue also involved.

However, the on-water search efforts were halted after several hours due to bad weather.

Mr Higgins, and another man Derek Robinson, were the subject of a major search south of Port Lincoln earlier this month after nothing was heard from the pair for several days.

Their boat was eventually spotted off the SA Coorong and towed to shore.

The 57-year-old was subsequently fined $1000 fine for having insufficient safety equipment and no boat operators licence. He insisted he didn't ask to be rescued and that the pair "knew exactly where we were".

SA Police Commissioner Grant Stevens said while search operations would always be conducted there was an "element of frustration" that the state's resources had been called on again.

He said the first search cost in the order of $650,000.

"Search and rescue efforts will always be undertaken but there is an obligation that sits with all of us to act in a way that doesn't put ourselves at risk," Mr Stevens said.

"It's unfortunate we are doing this again for the same person in such a short period of time."

A plane from the Australian Maritime Safety Authority joined the search on Tuesday afternoon.

Paramedics and police also remained on standby on shore.

Australian Associated Press