The man, a 30-year-old Filipino named Jay-Nel Rosals was found on Friday afternoon two kilometers (1.2 miles) from Kodakara Island, the Coast Guard said. He was taken to hospital, and is alive, walking and talking, it added.
He is only the third person to be found after the Gulf Livestock 1 transmitted a distress signal early Wednesday when it was about 185 kilometers (115 miles) west of Amami Oshima island.
A lone Filipino sailor was rescued late Wednesday, after more than half a day in the water. He was in good condition, the Coast Guard said.
A second crew member was found floating unconscious on Friday morning near Japan’s Amami Oshima island, about midway between Okinawa and Kyushu, Japan’s southernmost main island. He was taken to hospital, according to a Coast Guard statement sent to CNN, but a later statement from the Coast Guard said that he had died.
Just after 4 p.m. local time (3 a.m.) on Friday — around the same time that Rosals was located — rescuers found an empty lifeboat further out to sea, at around four kilometers east of Kodakara Island. Japan’s Coast Guard also said that they found some oil spillage around 150 kilometers from Amami Oshima Island.
The Coast Guard also found a body of a cow near Amami Oshima island on Friday. According to the Coast Guard, the search and rescue operation is ongoing, and no other cow carcasses have been found.
The area in the East China Sea 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.
The 133.6-meter-long (438 foot) ship, crewed by 39 Filipinos, two New Zealanders and two Australians, was sailing from Napier, New Zealand, to Tangshan, China, according to the authorities in Japan, New Zealand and Australia.
The Panamanian-flagged ship left New Zealand on August 14 with a cargo of more than 5,800 cows, according to New Zealand’s Ministry of Foreign Affairs and Trade.
A second storm in the region, Typhoon Haishen, is expected to strengthen to the equivalent of a Category 4 hurricane by the end of the week. It’s expected to threaten Kyushu on Sunday, and potentially affect the Korean Peninsula Monday.
Japan’s meteorological agency is warning that the storm could be the third biggest to hit the country since records began almost 70 years ago.
A New Zealand animal rights group said the Gulf Livestock 1 incident illustrates why the export of live animals should not be permitted.
“These cows should never have been at sea. To make matters worse they’re likely all pregnant,” said Marianne Macdonald, campaigns manager for animal rights group SAFE NZ.
“This is a real crisis, and our thoughts are with the families of the 43 crew who are missing with the ship. But questions remain, including why this trade is allowed to continue,” Macdonald said in a statement.
Correction: Previous versions of this article gave the incorrect date for when the ship set sail. It was August 14.
CNN’s Angus Watson, Eric Cheung, Junko Ogura and Thornton Chandler contributed to this report.