The man, who was later pronounced dead, was found unconscious and floating face down about 75 miles north-west of Amami Oshima in the East China Sea. A total of 41 crew members are still missing after another man was rescued on Wednesday.
Rescuers have been looking for the Gulf Livestock 1 ship and its missing crew since it sent a distress signal early on Wednesday.
Takahiro Yamada, a senior spokesman for the regional coast guard headquarters, said the second man’s nationality and crew status is unknown.
The spokesman said rescuers also spotted dozens of cow carcasses floating in the area. So far, he said he was not aware of reports of any carcasses washing ashore on the Japanese coast.
The 11,947-tonne ship, its 43 crew and 5,800 cows left New Zealand in mid-August heading to Tangshan on China’s eastern coast.
A Filipino crew member, 45-year-old chief officer Edvardo Sareno, was rescued late on Wednesday.
He told rescuers the ship stalled when an engine stopped, then capsized after being hit by a powerful broadside wave before sinking.
Coast guard officials quoted Mr Sareno as saying that he put on a lifejacket and jumped into the sea, and that he has not seen any other crew members since then.
“Thank you, thank you very much,” he told rescuers as he was escorted on to a bigger ship, where he sat on a blue tarpaulin, wrapped in blankets and taking a bottle of water.
“I’m the only one? No other one?” he asked the rescuers, then added: “I’m so sorry… (I’m) so lucky.”
The total crew included 39 from the Philippines, two from New Zealand and two from Australia.
Rescuers in four coast guard boats and an aircraft as well as divers joined Friday’s search and rescue operations.
A bundle of orange rope and a life jacket carrying the ship’s name were also recovered, according to a coast guard statement.
Typhoon Maysak was blowing by southern Japan at the time of the sinking. The ship’s automated tracker showed it sailing in high winds of 66mph at its last known position, according to the ship-tracking website MarineTraffic.com.
The ship’s operator, Gulf Navigation Holdings PJSC, based in Dubai, in the United Arab Emirates, declined to comment.
The company, traded on the Dubai Financial Market, says it owns and operates chemical tankers, livestock vessels and other ships.
Another powerful typhoon is approaching southern Japan over the weekend.
