A 69-year-old man survived 22 hours lost at sea off southern Japan, sat on the stern of his capsized boat and cloaked in a tarpaulin to protect him from the wind and spray.

A video of his rescue, filmed by the Japan Coast Guard, showed one of his rescuers jump into the choppy grey water and swim towards the boat, as the man sat hunched, virtually motionless, propped up against the rudder.

The man, whom the coast guard said was Japanese, remained almost monosyllabic as his rescuer clambered up alongside him on the upturned hull.

A rope was attached, and a Coast Guard launch reeled the upturned boat close enough for its crew to haul the man and their crewmate aboard.

The water temperature was almost 23 degrees Celsius, but there was a blustery wind and the sky was filled with heavy rain clouds.

The man, whose name has not been released by authorities, had been working alone on the boat for a port construction project off Yakushima when it capsized on Saturday afternoon.

His co-workers contacted the Coast Guard, and he was found a day later, around 30km off Onoaida Port in Yakushima.

The Coast Guard said he had suffered a minor ankle injury.