Japanese authorities racing to find dozens of missing sailors from a cargo ship that sank in a typhoon found a second survivor on Friday, as another, much more powerful storm drew near.

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

A first survivor was found on Wednesday evening, with the body of a second crew member recovered at sea early Friday, as hopes began to fade for the operation and powerful Typhoon Haishen barrelled towards the area.

But the coast guard said they found a second survivor on Friday afternoon, a 30-year-old Filipino who 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.

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.

Precisely when and where it sank remained unclear.

Dramatic footage of Wednesday's rescue showed the man bobbing in the open ocean in an orange lift jacket and rescuers battling violent waves to pull him on to their boat with a rope.

After he was moved to a larger boat and wrapped with blankets, he asked for water and thanked his rescuers.

"I am the only one? No other one?" he asked.

The ship is believed to have been caught up in Typhoon Maysak, which moved through the area with gusts of up to 160 kilometres per hour.

But Haishen is a much stronger storm, and is expected to affect Japan from late Saturday, with winds of up to 290 kilometres per hour (180 miles per hour), making it a "violent" storm -- the top level on Japan's classification scale.

'Water started coming in' 

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

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

In Manila, relatives of the crew were waiting desperately for news.

Captain Dante Addug's sister told AFP that he had been in touch with his girlfriend shortly before the boat sank.

"He told her there was an engine failure but they were able to restart it after an hour," Fredelyne Sanchez said.

"But then the big waves worsened and water started coming in."

Four coastguard vessels, a defence ministry plane and specially trained divers are involved in the search.

But it is unclear how much longer their efforts can continue, with Haishen heading towards the area.

The storm was expected to begin affecting areas including Okinawa in southern Japan and parts of western Kyushu from Saturday night to Monday, and the government warned residents to prepare.

"In the region that the typhoon is approaching, record rains, storms, high waves and high tides are feared," government spokesman Yoshihide Suga said Friday.

In preparation, water was being emptied from behind dams to make room for heavy rainfall and a quick response system to warn residents was being activated, he added.

The Gulf Livestock 1 crew was made up of 39 Filipinos, two New Zealanders and two Australians. The boat was travelling from Napier in New Zealand to the Chinese port of Tangshan.

It had experienced engine problems before: a 2019 observer report by Australian authorities noted that the boat was forced to drift at sea for 25 hours after an issue with its main engine while en route to China.