The ship, Gulf Livestock 1, is believed to have capsized in the East China Sea after being caught up in the storm. So far only one person on board has been rescued. The Japanese coast guard continue to search for the rest of the crew as well as the remains of the ship, but has so far failed to find any more survivors.
The cargo ship sent out a distress signal west of Amami Oshima island after being caught up in Typhoon Maysak, which brought winds of nearly 140mph, heavy seas and torrential downpours.
The ship, a Panamanian-flagged cargo vessel built in 2002, disappeared shortly after the signal was sent.
The one survivor was found alive adrift in the middle of the sea, with the ship no where to be seen.
The Japanese Coastguard shared a picture of the rescue mission, where the crew member was seen being hauled from the choppy seas.
The rescued crew member, 45-year-old Sareno Edvarodo told the Japanese Coastguard the vessel lost an engine before it was hit by a wave and capsized.
Crew had been instructed to put on life jackets.
Mr Edvardo, a chief officer from the Philippines, said he jumped into the water as the ship capsized, but he did not see any other crew members before he was rescued.
Three vessels, five airplanes and two divers have been deployed to continue the search for the rest of the crew, which consisted of two Australians, two New Zealanders and 39 Filipinos.
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New Zealand animal rights organisation SAFE said the tragedy demonstrated the risks of the live animal export trade.
Campaign manager Marianne Macdonald said: “These cows should never have been at sea.
“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.”
Typhoon Maysak, which made landfall early on Thursday in the South Korean port city of Busan, is one of the strongest storms to hit the region in years.
It is currently moving north and made a second landfall at Kimchaek in North Korean, before weakening as it tracked into north-east China.
Additional reporting by Maria Ortega