As many as 600 whale sharks a year are killed to supply one factory alone in China, a three-year undercover operation has revealed.

Paul Hilton, a conservation photo journalist and co-director of Hong Kong based NGO, WildLife Risk made three trips between 2010 and 2013 to the town of Puqi in China's south east following a tip-off.

"We decided to set up a small seafood trading company and we organised a business trip," he told Radio Australia's Asia Pacific program.

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"We met with a gentleman called Mr Li who runs the China Wenzhou Yueqing Marine Organisms Health Protection Foods Co Ltd and there (to) the processing plant and the courtyard was just full of giant whale shark fins."

Whale shark hunting as well as the sale and export of products are banned in China which has signed the Convention on International Trade in Endangered Species (CITES).

Despite that, the Fisheries authorities say they lack the resources to stop the trade.

"Recently this week there was a spokesperson who wanted to remain anonymous from the Chinese Fisheries side saying they are just totally understaffed and they don't have the resources to do more for endangered species," Mr Hilton said.

"So there's loopholes all through the system, people are taking backhanders."

The whale shark is the largest living fish and is protected under Australian waters. ( Paul Hilton/Greenpeace )

The fins and meat stay in China while customers for the oil and skins are in North America and Europe.

The work by WildLifeRisk backs up a report from July 2012 by Murdoch University's director of EcOcean, Brad Norman.

He collaborated with researchers at Shandong University in a survey of 2,500 fisherman in eight provinces and found a potential crisis is facing the endangered whale sharks.

"The chief of Hainan Fisheries and a couple of the interviewees believe that there are more than one thousand whale sharks caught in coastal waters around China. And that's a massive number of sharks," Mr Norman said.

"And given the area where WildLifeRisk went to is the sort of shark capital of China, a figure of 600 for one factory (means) there's obviously the potential to be many factories taking large numbers of whale sharks at the same time."

About whale sharks The world's largest living fish, grows up to 18 metres and weighs about 20 tonnes

The world's largest living fish, grows up to 18 metres and weighs about 20 tonnes Protected in Australian waters, under state and federal legislation

Protected in Australian waters, under state and federal legislation Despite their huge size, these gentle giants are harmless filter feeders that eat plankton

Despite their huge size, these gentle giants are harmless filter feeders that eat plankton Ningaloo Marine Park in WA is one of the few places in the world where they appear regularly

Mr Norman says studies of the whale shark's migratory habits has just started, making it difficult to assess the impact of one country's harvesting on other places.

"Given that they're highly migratory on a global scale, protection in one country will not assist the conservation of these animals if they move out of that jurisdiction and they're in an area where they're actively hunted," he said.

"And this is our issue in some locations including China where large numbers of whale sharks are being hunted and it will affect the global population.

"The global population of whale sharks is presently unknown however we can see trends and the trend has been in recent years that the numbers are declining."

Taiwan also killed whale sharks until about six years ago, although its thought some illegal hunting and a blackmarket trade continues.

Mr Hilton says China has the opportunity to shut down its illegal factories.

"For that to happen though I think there has be a lot of dialogue behind closed doors. Now we've actually shone a light on the issue, now hopefully that dialogue can start," he said.

Swimming with whale sharks has become a famous tourist attraction at Western Australia's Ningaloo Reef and the animal is the state's marine animal emblem.