He was conscious and able to walk by himself, they said.
The ship, with a cargo of almost 6,000 cattle, sent a distress call from the west of Amami Oshima island in southwestern Japan on Wednesday as Typhoon Maysak lashed the area with strong winds and heavy seas.
The Japanese coastguard said the second survivor is a 30-year-old Philippine national, who was working as a deckhand on the ship.
The corpse of a cow has also been seen floating in the waters nearby, along with an empty life raft.
Rescuers on Friday also found a man floating in the sea unconscious, but he was later pronounced dead.
"I'm the only one?" he asked rescuers after being pulled from the water.
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.
The 11,947-ton Gulf Livestock 1 cargo vessel.
His wife, Catherine Sareno, a schoolteacher, said she was so anxious about her husband that she prayed all night, rosary in hand, after learning the ship sank in stormy weather.
In the wake of the accident, New Zealand said it was temporarily suspending live cattle exports.
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The captain of Gulf Livestock One sent a distress call to the Japanese Coast Guard at about 1.20am on Wednesday.
The rest of the crew - mainly Filipinos, with two Australians and two New Zealanders - remain missing.
The last movements of the cargo ship that went missing after sending a distress signal during Typhoon Maysak have been revealed by marine authorities. Two people, both Filipino, were rescued Friday and one body was recovered. "It's hard for somebody like me for a day to pass without any news".
Three vessels, four airplanes and two divers were taking part in the search, the coastguard said.
He said the ship lost an engine before it was hit by a wave, causing it to capsize.
The FleetMon report also noted some concern from local residents about the ship's extended stay at Cesme port, because livestock on a previous voyage had been found to be infected with anthrax. The Gulf Livestock 1 was capsized after losing an engine in the stormy East China Sea. The boat was traveling from Napier in New Zealand to the Chinese port of Tangshan.
Camera IconWaves hit a shore in Nagasaki as an offshore typhoon passed through southern Japan.
The Filipino crew member was rescued late Wednesday after Japanese navy surveillance aircraft spotted him wearing a life vest and waving while bobbing in the water.
"Our hearts go out to those onboard and their families at this time", a Gulf Navigation spokesman said.
Dubai-based Gulf Navigation Holding, the owner and operator of the stricken ship, issued a statement expressing sympathy for those affected by the disaster.