Taiwan's fishing industry was "out of control", environment advocacy group Greenpeace said Thursday, with shark finning still rampant as well as labour and human rights abuses.

Taiwan has one of the world's biggest tuna fishing fleets and the new Greenpeace investigation is just the latest criticism of its practices.

The European Union warned Taiwan last October that it would face economic sanctions if it did not tackle illegal fishing within six months -- a period which is almost over.

"These investigations paint a comprehensive picture of an industry in crisis," said Yen Ning, campaigner at Greenpeace East Asia.

"Despite talking the talk, Taiwan's Fisheries Agency appears incapable of monitoring the out-of-control tuna industry."

The year-long probe into Taiwan's distant water tuna fisheries revealed the "devastating impacts on marine life and people's lives" from the industry, Yen added.

Crew on Taiwanese vessels -- which include as many as 160,000 migrant workers -- endure "horrendous" working conditions and physical abuse, withheld payments and exploitation by recruitment agents, the report said.

Greenpeace said foreign crews' labour rights are not protected by any regulations, with workers recounting tales of being beaten by captains and working more than 20 hours a day for months on end.

Taiwan's Fisheries Agency -- the government division overseeing the industry -- did not have an immediate response to the Greenpeace allegations.

Commenting on the expiring warning from the EU, the agency's deputy chief Huang Hung-yan said: "They know that Taiwan has done a lot of work in this area. We communicate frequently."

An EU ban on Taiwan fishery imports could cost the island 13 million euros ($14.6 million) a year, the European Commission, its executive arm, has estimated.

Despite warnings against illegal shark fishing, Greenpeace said its investigation discovered 16 cases of shark finning in just one Taiwanese port over a three-month period.

Legislation passed in 2012 requires fishermen to ship back entire shark carcasses, preventing them from just slicing off the fin -- a delicacy in Chinese cuisine.

But Greenpeace said in September it had discovered a haul of illegal shark fins on a Taiwanese ship near Papua New Guinea.

The Fisheries Agency rebuked Greenpeace for boarding a Taiwanese vessel without permission from the government, but promised it would investigate claims the ship was fishing illegally.

The report Thursday also raised concerns about Thailand, one of the biggest markets for Taiwan's catch, where labour rights abuses have been revealed in its seafood processing industry.

Thailand was also warned of potential fishery sanctions by the EU last year.

"The fishing industries of both Taiwan and Thailand have been shown to have human rights problems," said Yen of Greenpeace.

"Seafood lovers everywhere may be eating tuna tainted by human exploitation and environmental crime, and they'd never know."