Australia's bid to take Japan to the International Court of Justice over its so-called scientific whaling program may be about to get a boost.

Two former Japanese whalers have told the ABC's Foreign Correspondent program of systemic embezzlement by crewmen onboard the country's whaling ships.

Speaking for the first time, they say that crew members are taking what amounts to hundreds of kilograms of prime cuts of whale meat, either for personal consumption or to sell on to restaurants.

One whistleblower, who asks to be called Kujira San - Japanese for "Mr Whale" - says this practice even extends to the body in charge of the scientific whaling program.

Kujira San, a former crewman on Japan's whaling fleet flagship the Nisshin Maru, says what he is revealing could get him killed because his former shipmates do not tolerate those who break the code of silence.

"First, when the ship returns to Japan and arrives in the port, a transport truck is waiting. The crewmen will then pack the whale meat they stole into a cardboard box. One person carried off 500 to 600 kilograms," he said.

He claimed some crewmen made a fortune from reselling the meat.

These are explosive allegations which, if true, undermine much of Japan's claim that its whaling program is centred on scientific research.

Kujira San's claims are backed by another man, T San, who has more than 30 years of experience on whaling ships.

"It happened on the container on the bridge. I had to check the temperature every day and when I went in there, there was a staff member from the Institute of Cetacean Research packing something," he said.

"When I yelled, 'What are you doing?' he then tried to hide the package by spreading his arms out.

"It was red meat from the tail. That is the highest quality whale meat."

The Institute for Cetacean Research is the body in charge of Japan's scientific research program, and both whaling whistleblowers allege serious corruption inside the program.

Junichi Sato works for Greenpeace Japan. He and a colleague, Toru Suzuki, tracked the smuggled whale meat, intercepting one box containing 23 kilograms of prime cuts.

"We started following the boxes offloaded from the Nisshin Maru to the house of the crew members," Mr Sato said.

They showed the Japanese media, then took the meat to prosecutors, who promised to investigate the alleged theft by crew members.

But a month later the two Greenpeace activists were arrested and charged with stealing.

Today Junichi Sato and Toru Suzuki, who are known as the Tokyo Two, are appearing at the final day of their trial.

They face up to 10 years in jail as well as the rage of many of their compatriots.

In Japan blowing the whistle on suspect practices inside the so-called scientific whaling program can mean being branded a traitor as well as possibly going to jail.