The incident, involving 17 crewmembers from China, 17 from Indonesia and five from the Philippines, happened around 3am on Tuesday some 4,600km northwest of Australia, Chinese state broadcaster CCTV said.
Chinese leader Xi Jinping and Prime Minister Li Qiang have ordered Chinese diplomats abroad, as well as the agriculture and transportation ministries, to assist in the search for survivors.
"All-out efforts" must be made in the rescue operation, Xi was quoted as saying by the official Xinhua News Agency.
It's not yet clear why the vessel capsized.
Several ships and an Australian Defense Force P-8A Poseidon aircraft have been searching the area.
The Indian Ocean stretches from South Asia and the Arabian Peninsula to east Africa and Western Australia.
No survivors or life rafts have been spotted so far.
The Australian Maritime Safety Authority is coordinating the search in what it described as a remote part of the Indian Ocean, about 5,000km northwest of the coastal city of Perth.
The agency received a distress beacon signal from the fishing vessel at about 5.30am on Tuesday, Australian time.
Weather conditions in the area on Tuesday were "extreme" but had improved by Wednesday, AMSA said.
A Perth-based Challenger rescue aircraft will drop a buoy to help with drift modelling to further assist in the search.
Chinese Foreign Ministry spokesperson Wang Wenbin said additional rescue assets were on their way to the scene.
"We will continue to take all measures possible with all parties to search and rescue the missing persons," Wang told reporters at a daily briefing Wednesday.
"The Chinese side thanks the Australian maritime search and rescue department for promptly dispatching aircraft and coordinating passing foreign ships to participate in the search and rescue."
The capsized hull was spotted and the transmitter detected more than 1,000km south of Sri Lanka, with the nearest port appearing to be the island chain of the Maldives, about 500km to the north of the search area.
The vessel is believed to be the Lu Peng Yuan Yu 028 which is based in the eastern coastal province of Shandong and operated by the Penglai Jinglu Fishery Company.
China is believed to operate the world's largest fishing fleet.
Many of stay at sea for months or even years at a time, supported by Chinese state maritime security agencies and a sprawling network of support vessels.
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