When police in East Timor caught a large fleet of Chinese fishing boats last year, with thousands of dead sharks on board, the evidence of illegal fishing — on a massive scale — seemed indisputable.

But after a nine-month investigation the crew, the boats and the multi-million-dollar haul are gone, having been released and allowed to sail home to China — apparently not guilty of any wrongdoing.

A US$100,000 ($135,300) payment apparently secured their release. But just who paid it, and where has the money gone?

The dawn raid, involving police from East Timor and Australia, was captured on camera and followed months of surveillance by the activist group Sea Shepherd, whose ship the Ocean Warrior had tracked the Chinese fleet off East Timor's south coast.

It was the Ocean Warrior that took police out to sea last September to raid the boats, where they found "thousands and thousands" of frozen sharks "on every single vessel", including leopard sharks and the endangered hammerhead sharks which are protected under the CITES Convention.

The 15 boats and their Chinese crew — owned and employed by Honglong Fisheries — were immediately impounded and detained, while prosecutors in East Timor investigated their activities and prepared a legal case against them.

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

But inexplicably, East Timor's District Court in Baucau has now released the crew without charge and allowed them to take the boats back to China — in return for a US$100,000 guarantee — on the grounds the crew did nothing wrong.

One Chinese captain remains in detention, but sources have told the ABC they expect he too will soon be freed.

The ABC understands that the huge catch of frozen shark — far from being confiscated — has gone with the boats to China, where it could be worth millions of dollars.

East Timor's former Minister for Agriculture and Fisheries, Estanislau da Silva, has told reporters in Dili that there was no evidence the crew had violated Timorese law, and that the court released them because they did not have protected sharks on board.

But critics including Sea Shepherd say the decision "reeks", and raises questions about China's pervasive influence in East Timor.

They question where the money was paid. One key source told the ABC there appears to be no receipt or record of the money being paid into the relevant government coffers.

It is understood East Timor granted the 12-month fishing licence to Honglong Fisheries in 2016 for less than US$500,000 ($677,025). Yet the company which effectively owns Honglong Fisheries — Pingtan Marine — has boasted that each of its fishing boats can generate up to US$1 million ($1.35 million) in annual revenue.

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

Against that background, a US$100,000 payment to free the 15 boats and their crew would barely make a dent in its profits, and simply be written off as the cost of doing business in East Timor.

Sea Shepherd has also questioned — if the crew had done nothing wrong — why they were asked to make any payment at all.

"Why pay $100,000? Something is not right," said Gary Stokes, Sea Shepherd's Director for Asia.

"I think it was a smokescreen to let them go, so people didn't kick up a fuss. And as soon as they've gone the minister has come out and said yes, we let them go. They did nothing wrong."

Mr Stokes also rejects the court's claim that there were no sharks on board.

"Where we're very angry, is that the laws are very, very clear in Timor. The endangered species that are listed on CITES, which include the hammerhead, are protected and are forbidden to be caught," he said.

"When we boarded (the boats) … we instructed the (Timorese police) and they went to the forward freezer and they dug down deep and they actually found hammerhead sharks.

"Here we have the national police holding the evidence, with photos of the evidence presented to the court in Baucau, and for some reason it was thrown out of court, that they didn't violate any of the laws of Timor Leste."

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

Indeed, it was not the first time Honglong Fisheries had been accused of illegal fishing in East Timor. Sea Shepherd began its surveillance after the same fleet was documented in February 2017 offloading massive quantities of shark to a mothership, just 500 metres from the Timorese coast.

Yet Mr Stokes says on that occasion the company was fined a mere US$500 ($677) and told "don't do it again".

"What they did was they would just go offshore, and they would do the transhipments offshore where nobody would ever see them," he said.

"Every two-to-three months a ship was coming, a big refrigerated cargo ship, and it was literally meeting them offshore, taking all the sharks.

"The whole enterprise is illegal. But their partnership with the Timorese officials — for peanuts — reeks."

The same mothership — the Fu Yuan Y Leng 999 — was later caught in the Galapagos Islands with 300 tons (272 tonnes) of shark on board, much of which presumably came from waters off East Timor.

The ship remains impounded in Ecuador, where the crew were jailed. But the Chinese crew in East Timor are now free.

East Timor is not a signatory to the CITES convention, which prohibits fishing of endangered species.

In 2014 Pingtan was expelled from Indonesia after two marine companies it controlled there were linked to allegations of fraud and bribery. ( Supplied: Jake Parker/Sea Shepherd )

But Sea Shepherd says Honglong Fisheries clearly broke East Timorese law in multiple ways, by breaching the terms of its fishing licence, which was for tuna, not shark.

It says its surveillance showed the crew were repeatedly laying gill nets on the ocean floor, rather than drift nets — in violation of its licence — allowing it to sweep up bottom dwelling species including sharks, rather than tuna. It estimates that 95 per cent of the catch found on board the boats was shark, including hammerheads.

The ABC has sought comment from Estanislau da Silva, who since a change of government in East Timor is no longer the minister for Agriculture and Fisheries. A new minister is yet to be appointed.

Pingtan linked to company accused of slavery, torture and money laundering

Pingtan Marine is a US NASDAQ-listed company based in Fuzhou, China, with a shady record on fishing and human rights.

In 2014 Pingtan was expelled from Indonesia after two marine companies it controlled there were linked to allegations of fraud and bribery, as well as the illicit fishing and trade of protected species.

Indonesia's fisheries ministry had found that one of the companies, Dwikarya, had tortured crew members, engaged in forced labour and committed other serious breaches of labour laws. Dwikarya denied the allegations, but its fishing licence was cancelled.

Indonesia's Supreme Court also found evidence of violent "torture ships" that "implicated Pingtan in the modern-day slavery that has infected pockets of South-East Asia's fishing industry," according to a report to NASDAQ investors last year, by the research company Aurelius Value.

Sea Shepherd says as well as the Chinese crew — who were detained in East Timor for nine months, until their release this month — most of the deck crew came from the Philippines, who were allowed to leave after the boats were impounded last year.

Mr Stokes says the Filipinos are still waiting for payment from Honglong Fisheries.

The ABC has tried repeatedly to contact officials at both Pingtan and Honglong Fisheries, but neither company has responded.

In a statement last month Pingtan rejected specific allegations it had made false statements to East Timor during the licensing process in 2016.

"The (Ministry of Agriculture and Fisheries) is alleging and is investigating whether false statements were made during the licensing process and the vessels were simultaneously registered in Indonesia. The company disputes these allegations," the statement read.

Mr Stokes says Sea Shepherd is trying to track the 15 Chinese boats — assuming they are returning to China — in the hope it can still bring the company to justice, and prevent the trade of its huge, illicit catch.