A cargo ship carrying 43 crew and about 6,000 cows sank at sea after transmitting a distress signal during a typhoon off Japan, according to a survivor rescued by the country's coast guard.

The Gulf Livestock 1 issued a distress call early Wednesday from a position 185 kilometres (115 miles) west of Japan's Amami Oshima island.

The area was being battered by the powerful typhoon, equivalent to a Category 4 hurricane with winds of at least 130 mph, at the time the ship went missing.

Late Wednesday, coast guard rescuers located one survivor, a man identified as a 45-year-old Filipino chief officer, who said he had put on a life jacket and dived into the sea after a warning announcement on board.

He said one of the boat's engines had stalled and a wave then overturned the ship, which later sank, the coast guard said in a statement.

There were no details on when and where the ship sank, but the man said he had not seen other crew members while waiting to be rescued.

A rubber boat was spotted late Wednesday in the area being searched for survivors, but the coast guard said they had not confirmed if it was linked to the ship.

Japan's meteorological agency warned that the storm could be the third biggest to hit the country since records began almost 70 years ago.

(With input from AFP)