Japan's Fisheries Agency has admitted its officials accepted gifts of whale meat from the body that runs the country's so-called scientific whaling program.

Six months ago the ABC broadcast allegations by two whaling crew members that officials and crew were illegally taking thousands of dollars worth of whale cuts.

At the time the Fisheries Agency denied the allegations, but it has now reprimanded five of its officials for taking more than $3,000 worth of whale meat.

Agency spokesman Toyohiko Ota has publicly apologised for the scandal.

"I deeply apologise for this act in which officials took whale meat," he said.

"It's an act for which we will lose credibility. We will take prevention measures so it will never happen again," he added, with a deep bow of apology.

The original allegations, broadcast on ABC TV's Foreign Correspondent program, undermined Japan's claim that its whaling program was purely for science.

"One crew member would take home 500 to 600 kilograms of whale meat as if it was normal," one of the whistleblowers said.

"That's a little too much to eat at home. Some people give it to their neighbours, others are obviously selling it. I heard a story that one crewman built a house from selling whale meat."

At the time the allegations were dismissed by the Institute for Cetacean Research, which helps run Japan's whaling program. The Fisheries Agency also denied that officials or crew took whale meat for personal consumption or profit.

Although the agency now admits that more than $3,000 worth of meat was taken, Greenpeace and the two whistleblowers believe that is just a fraction of the amount that has been embezzled.

And today's admission is a massive boost for the two Japanese Greenpeace activists known as the Tokyo Two.

Four months ago, Toru Suzuki and Junichi Sato were given suspended jail sentences for theft.

Their crime was to track and then intercept a box of whale meat taken by a crew member. They later handed the box over to prosecutors.

But instead of the crewman being charged, Suzuki and Sato ended up in the dock and with a criminal conviction.

Sato spoke to the ABC outside the court after his conviction in September.

"It's outrageous that the court actually recognised that there is some ambiguous handlings of whale meat in the whaling industry," he said.

"Even so, they are trying to punish us [with] one year in prison and three years in suspended. It is outrageous, and if this is a democratic country, this shouldn't be happening."

The Tokyo Two have now challenged that conviction, and this admission from the Japanese Fisheries Agency is certain to be a key plank of their appeal.

Greenpeace Australia's Stephen Campbell says the agency's admission shows there is no such thing as scientific whaling.

"We know in fact that the Japanese whalers toss whale meat overboard as well," he told ABC News 24.

"All of this activity in the Southern Ocean is really largely for show and to keep the Japanese Fisheries Agency alive and to feather the nests of the few officials."