Fifteen Chinese fishing boats have been caught with thousands of sharks in Timor-Leste waters in a joint raid by local police and activist group Sea Shepherd.

Key points: Sea Shepherd says boats were "supposed to be catching fish" but clearly targeting sharks

Sea Shepherd says boats were "supposed to be catching fish" but clearly targeting sharks Boats have been operating under licence from Agriculture and Fisheries Ministry

Boats have been operating under licence from Agriculture and Fisheries Ministry Sea Shepherd patrolling to ensure boats do not leave Timor-Leste waters

Sea Shepherd's Timor-Leste campaign leader Gary Stokes said the group's Ocean Warrior helped armed Timor-Leste National Police (PNTL) officers conduct a raid on Saturday morning.

"We found thousands and thousands of sharks on every single vessel," he said.

"They were setting bottom gill nets that were basically weighted to the sea bed.

"They were supposed to be catching fish, but it was very, very clear that they were just targeting sharks."

Sea Shepherd worked closely with the East Timor National Police in the raids. ( Supplied: Jackson Frauenfelder/Sea Shepherd )

Ocean Warrior is currently patrolling waters near Vemasse, according to Mr Stokes, to make sure the Chinese boats do not leave Timor-Leste waters.

"East Timor is a very poor country and they have no naval assets at all, no patrol vessels, no warships to go out and patrol their waters," he said.

"These vessels basically have carte blanche to cruise their waters and take whatever they want."

'Why do the Timorese have a contract with this company?'

The Chinese boats, owned by Pingtan Marine Enterprise, have been operating under a licence from Timor-Leste's Agriculture and Fisheries Ministry, which expires in November this year.

The company is listed on the United States NASDAQ and has previously been banned from fishing in Indonesian waters.

Sea Shepherd staff document the shark kill. ( Supplied: Jake Parker/Sea Shepherd )

Fundasaun Mahein, a local not-for-profit organisation analysing maritime security policy in Timor-Leste, said the fishing licence had been granted to Pingtan Marine Enterprise's related entity Hong Long Fisheries.

"This kind of thing was happening several months ago and now it has happened again," Fundasaun Mahein executive director Nelson Belo said.

"Since then the Government's made a statement, but they have not implemented it.

"We would like to ask the Government to tackle it seriously."

Mr Belo said Timor-Leste should immediately suspend the licence for the Chinese fishing boats.

"This company was suspended by the Indonesian Government and not allowed to go into its waters," he said.

"Why do the Timorese have a contract with this company?"

Sea Shepherd says the fishing vessels were using anchored gill nets to target bottom dwelling species such as sharks. ( Supplied: Jake Parker/Sea Shepherd )

Timor-Leste authorities inspected the 15 boats in February, after a video from Portuguese news agency Lusa showed shark hauls on board.

The inspections revealed more than 40 tonnes of shark, which the Government said could contravene Timor-Leste law and the fishing licence conditions.

"The Government will follow the due process to ensure the licence holders are acting correctly," a spokesman said at the time.

Timor 'needs its fish to feed itself'

The ABC understands the Government held an "emergency meeting" to discuss the latest shark haul on Wednesday and the Agriculture and Fisheries Minister Estanislau da Silva has been contacted for comment.

Timor-Leste's new Prime Minister is expected to be sworn in on Friday, with Mari Alkatiri nominated for the role by the new coalition between his Fretilin party and the Democratic Party.

After hunting for the fleet of fifteen vessels for two weeks, the Ocean Warrior found them 150km south of East Timor. ( Supplied: Jake Parker/Sea Shepherd )

Negotiations about the composition of Timor-Leste's new Government have been taking place since the country's parliamentary elections in July.

Unmonitored large-scale fishing licences could compromise Timor-Leste's food security and developing marine tourism industry, according to Karen Edyvane from Charles Darwin University, a visiting professor at the National University of Timor-Leste.

"Timor-Leste desperately needs its fish to help feed itself," she said.

"As one of the world's most food insecure and malnourished nations, improving domestic seafood supply and developing Timor-Leste's domestic fisheries is a national priority.

"Illegal fishing on an industrial-scale, can wipe out these critical resources in just a few years."

Pingtan Marine Enterprise has been contacted for comment.