Dozens of people including two Australians are missing and feared drowned off the coast of Japan after their livestock ship capsized amid stormy weather from Typhoon Maysak.

Filipino chief officer Sareno Edvardo, the only one of the 43 crew members on board rescued by Japan’s Coast Guard, said the 11,947-tonne cargo vessel carrying 5800 cows has sunk.

The ship was engulfed by an enormous wave after one of its engines stopped running, causing it to capsize and sink, Mr Edvardo, 45, told the Coast Guard.

He put on a lifejacket before jumping into the waters of the East China Sea.

When help came, he could not locate any other crew members, Mr Edvardo said.

Grave fears are held for the two missing Australians, understood to be a vet and a stockhandler who were on board the Jordanian vessel Gulf Livestock 1 which was en route to China from New Zealand.

Lukas Orda, who previously worked at Gold Coast Equine Clinic and studied at James Cook University in Townsville, has been identified as the vet in several media reports.

Queensland equine vet Lukas Orda was believed to be on the Gulf Livestock 1 when it went missing. Photo: Facebook

The Department of Foreign and Affairs is assisting the families of the Australians.

“The Australian government is providing consular assistance to the families of two Australian crew members on board a cargo vessel reported missing in Japanese waters,” DFAT said on Thursday.

“Owing to our privacy obligations we are unable to provide further comment.”

The ship sent a distress call from west of Amami Oshima island in southwestern Japan on Wednesday as the region experienced strong winds, heavy seas and drenching rains from Typhoon Maysak as it headed towards the Korean peninsula.

An industry source told AAP the shipment was a New Zealand consignment which would fall under their regulatory authorities.

A survivor said the ship sank during rough weather. Photo: AAP

The shipment is believed to have been put together by Australasian Global Exports, a Melbourne-based exporter which operates across Australia and New Zealand. It’s understood the company has been contacting the families of the Australians.

Australasian Global Exports executive procurement director Graeme Turner declined to comment.

The exporter is believed to be responsible for employing stockhandlers and vets, with the shipping company employing the crew.

The vessel departed Napier in New Zealand on August 14 and was bound for the Chinese port of Jingtang, carrying 5867 cattle.

Its journey was expected to take about 17 days.

Japan’s coastguard said the 43 people on board also included 39 from the Philippines and two from New Zealand.

New Zealand’s foreign ministry is providing consular assistance to the families of the New Zealanders.

-with AAP