The search for the missing crew of a Chinese fishing vessel that capsized in seven-metre waves has been suspended as hopes fade for their recovery.

Australian aircraft and a multinational fleet of vessels had been searching a vast area of the Indian Ocean about 5000km northwest of Perth since Tuesday.

The Lu Peng - Yuan Yu is believed to have capsized about 3am AEST on Tuesday, with a distress beacon signal received by the Australian Maritime Safety Authority's Joint Rescue Coordination Centre (JRCC) in Canberra about 5.30am.

On Saturday the Australian Maritime Safety Authority (AMSA) said it called off the search.

"Despite significant multinational efforts, at this stage, of the 39 crew, two have been recovered, deceased," the agency said.

China's official Xinhua News Agency cited the country's transport ministry as confirming two bodies had been recovered on Thursday afternoon and that rescuers spotted objects including bags and plastic containers floating on the water.

The stricken vessel's crew consisted of 17 from China, 17 from Indonesia and five from the Philippines, AMSA said.

Weather conditions at the time were extreme, with the passage of Cyclone Fabian bringing 120km/h winds and seven-metre seas.

It is likely that the vessel capsized due to the cyclonic conditions.

On the same day, bulk carrier Navios Taurus sighted an upturned hull in the search area, along with some debris. No survivors were sighted.

During the four-day search, multiple aircraft were involved, including two from the Australian Defence Force, AMSA's rescue aircraft and two commercially chartered aircraft, with State Emergency Service observers from Perth on board.

A Chinese fishing vessel and three Chinese navy ships were also engaged in the search as well as merchant ships from Panama, Marshall Islands, Japan, Singapore, Hong Kong, and Liberia.

AMSA said it has been in continuous contact with the Maritime Rescue Coordination Centre (MRCC) in Beijing to coordinate search activities and plans, and ongoing recovery efforts will be led by China.