Gulf LifeStock 1 sent a distress signal early on Wednesday when it was about 185 kilometers (115 miles) west of Amami Oshima Island, midway between Okinawa and Kyushu, the main island in the far south of Japan.
The area in the East China Sea was hit by a powerful typhoon, the equivalent of a Category 4 hurricane with winds of at least 130 mph, at the time the ship was lost.
The rescued sailor was found late on Wednesday, after more than half a day in the water. The Coast Guard said he was in good condition.
The 133.6-meter (438-foot) vessel, with a crew of 39 Filipinos, two New Zealanders and two Australians, was sailing from Napier, New Zealand, to Tangshan, China, according to authorities in Japan, New Zealand and Australia.
The New Zealand Ministry of Foreign Affairs and Trade said the ship left New Zealand on August 17 with a cargo of more than 5,800 cows.
The Philippine Foreign Ministry said its consulate general in Osaka was monitoring the situation and coordinating with the Japanese Coast Guard, which was launching a second search and rescue mission.
A second storm in the region, Hurricane Haison, is expected to intensify to the equivalent of a Category 4 hurricane by the end of the week. It is expected to threaten Kyushu on Sunday, and potentially affect the Korean Peninsula on Monday.
The Japan Meteorological Agency has warned that the storm could be the third largest storm to hit the country since records began nearly 70 years ago.
A New Zealand animal rights group said the Gulf Lifestock 1 incident illustrated why live animals were not allowed to be exported.
“These cows shouldn’t have been at sea at all,” said Marian MacDonald, campaign manager at SAFE NZ. “To make matters worse, they are all likely pregnant.”
“This is a real crisis, and our hearts are with the families of the 43 crew members who went missing on board. But questions remain, including why this trade is allowed to continue,” MacDonald said in a statement.