Japanese authorities on Saturday resumed searching for dozens of missing sailors from a cargo ship that sank in a typhoon, but high waves caused by an approaching storm prevented boats from joining the operation.

The Japan coastguard found a second survivor on Friday after the Gulf Livestock 1, which was carrying 6,000 cows and had 43 crew on board, issued a distress call Wednesday near Amami Oshima island as Typhoon Maysak passed through the area.

Typhoon Haishen, a much stronger storm, is expected to affect Japan from late Saturday, with winds of up to 290 kilometers per hour, making it a "violent" storm -- the top level on the country's classification scale.

"We resumed our search operation this morning by dispatching an airplane," a local coastguard official said.

"But due to high waves, we could not send any patrol boats to the site."

"We still plan to send ships to join the search operation but it's not certain as another typhoon is approaching the region," he said, adding that there were no clues to the fate of the missing crew.

A first survivor was found on Wednesday evening, with the body of a second crew member recovered at sea Friday.

The crew was made up of 39 Filipinos, two New Zealanders and two Australians.

The boat, which had experienced engine problems before, was travelling from Napier in New Zealand to the Chinese port of Tangshan.

Haishen was barrelling towards Okinawa in southern Japan Saturday morning and on course for western Kyushu, prompting the government to warn residents to prepare.

Authorities on Minamidaitojima island instructed some 1,300 residents to evacuate as the storm was expected to hit the remote island, east of Okinawa.

"We urge all of our islanders to be on full alert as winds are getting stronger and expected to be violent," said Hidehito Iha, a local government official.

Footage showed troops escorting dozens of people at a heliport in Kagoshima, southern Kyushu, after they evacuated from another remote island by a military helicopter.

Public broadcaster NHK said major companies, including Toyota and Canon, decided to temporarily close their plants in Kyushu on Monday following the government warning.