The active search for dozens of sailors from a cargo ship that sank in a typhoon last week was called off Wednesday, Japanese authorities said, with two crewmen the only known survivors.

The Gulf Livestock 1, which was carrying 6,000 cows, issued a distress call last week as Typhoon Maysak passed through the area, launching a desperate search for the 43 crew on board.

The Japan Coast Guard had been racing to find the missing crew members as powerful Typhoon Haishen barrelled towards the area.

"We decided to shift our exclusive search for the missing people of the ship to a regular patrol search as of today's sunset time," the coast guard said in a statement.

"We didn't find any clues for them after today's search with a patrol ship and a plane," they said.

The two survivors were found last week, while the body of a crew member was recovered at sea on Friday.

The first survivor from the ship, a 45-year-old Filipino chief officer, told rescuers he had put on a life jacket and jumped into the sea after a warning announcement on board.

He said one of the boat's engines had stalled and the vessel was overturned by a powerful wave before eventually sinking.

The second survivor, a 30-year-old Filipino, was spotted in a life raft several kilometres from Kodakarajima, a remote island in southwestern Japan.

The man, identified as a deckhand, was reached by a patrol boat and was alone in the raft. He was able to walk unassisted, the coastguard said.

Precisely when and where the vessel sank remains unclear.

The ship is believed to have been caught up in Typhoon Maysak before Haishen swept towards Japan on Saturday, bringing with it winds of up to 290 kilometres per hour (180 miles per hour).

It moved to South Korea on Monday after slamming southern Japan with record winds and heavy rains.

There has been little sign of other survivors, with the coastguard spotting an empty rubber dinghy and a life jacket during their search.

Dead cows from the boat have also been seen in the waves.