Two members of Greenpeace are facing up to 10 years' jail in the latest skirmish to erupt over Japan's whaling activities.

While the whaling fleet and militant activists battle it out in the Southern Ocean, two men in Japan have been charged with trespassing and stealing whale meat.

Dubbed the "Tokyo Two", they say the whale meat was smuggled off a Japanese research ship with the full knowledge of government officials and it was headed for the black market.

Junichi Sato and Toru Suzuki intercepted the package, took it to the police and in turn were charged with theft.

But in a blow to Japan's judicial system, the ABC has obtained a United Nations report that says their detention contravenes international covenants on human rights.

Sato started surveying Japan's whaling-fleet flagship, the Nisshin Maru, on its return from an annual hunt two years ago.

"We were investigating the corruption in the whaling industry that is funded by taxpayer's money," he said.

"So we wanted to show the real face of the whaling industry, how corrupt this industry is, to the Japanese public."

Sato and Suzuki were acting on a tip-off from a former whaling crew member who blew the whistle on the alleged smuggling of whale meat off the ship and on to the black market.

In an interview recorded by Greenpeace, a former whaling crew member described how the meat was taken from the ship.

"Everyone knows, but it's not talked about in public" he said.

"They all do it, with tacit understanding. There are shipping company staff there too, but it seems that they see and pretend not to see."

Acting on this information, Sato and Suzuki tracked a package from the Nisshin Maru to a mail depot in northern Japan.

There they took the package which was marked "cardboard" and opened it. Inside there was no cardboard but 23 kilograms of salt-cured whale meat.

After showing the media, the activists handed the package to prosecutors, seeking charges of embezzlement against the crew.

Instead police arrested Sato and Suzuki for theft and trespassing.

"This is really a politically motivated arrest. We were trying to stop the bigger crime. This is not a theft case but it is about whaling on trial," Sato said.

The stakes are high for the activists. In Japan the conviction rate in criminal cases in 99.8 per cent.

Their defence lawyer, Yuichi Kaido, says he will argue a defence based on the men's NGO-affiliation.

"We will argue in court that these two men are members of an NGO," Mr Kaido said.

"There is a significant argument that research activities carried out by NGO members based on whistleblower evidence has the same rights and freedoms as investigative reporting by journalists."

He will also argue that the conditions the two activists were held under contravened international law.

Sato and Suzuki were held without charge for 23 days, questioned without a lawyer and interrogated for up to 12 hours a day while tied to a chair.

Embezzlement

The ABC's Lateline program obtained a report by the UN Human Rights Working Group on Arbitrary Detention.

The report found "the detention of Messrs Junichi Sato and Toru Suzuki is arbitrary and contravenes the dispositions contained in articles 18, 19 and 20 of the universal declaration of human rights and articles 18 and 19 of the international covenant on civil and political rights, to which Japan is a state party".

The UN working group also noted that they acted in the greater public interest because they sought to expose criminal embezzlement within the taxpayer-funded whaling industry.

The ABC approached both the Japanese Fisheries Agency and the prosecutors about the case of the Tokyo Two but both refused to comment.

The trial could cost both men their freedom, but Sato argues that will only bring more scrutiny of Japan's judicial system and its whaling program.

"Of course for private reasons I don't want to be in jail, but if they are putting us in jail, of course then we can fight back," he said.

"And [I] think we have more stronger arguments why this is a politically motivated arrest, because they want to simply shut us down."

The trial is expected to last several months.

Mark Willacy's full report can be seen on Lateline on ABC1 on Monday night