He once wielded a knife on the deck of a Japanese whaling ship, slicing apart the behemoths of the ocean in the name of "scientific research", while much of the rest of the world looked on in horror.

Now, as Japan pushes to overturn the 24-year ban on commercial whaling, the former whaler has come forward with allegations of widespread criminality among the men with whom he spent months in the freezing waters of the Antarctic.

Sent every winter to slaughter the mammals for research that Japan says is vital to our understanding of whale populations, the crewmen are instead seizing and selling prized cuts of meat to earn extra cash and, in at least one case, earn many more times their annual salary, says the whaler-turned-whistleblower.

He refers to himself only as "Kujira-san" (Mr Whale), a precaution necessitated by a genuine fear for his safety. But the personal risks will be worthwhile, he says, if it means the world learns the truth about the dark side of Japan's whaling industry.

"Even before we arrived in the Antarctic Ocean," he says of a recent expedition, "the more experienced whalers would talk about taking whale meat home to sell. It was an open secret. Even officials from the Institute of Cetacean Research [a quasi-governmental body that organises Japan's whaling programme] on the ship knew what was happening, but they turned a blind eye to it."

Kujira, who worked aboard the Nisshin Maru mother ship, saw crew members helping themselves to prime cuts of whale meat and packing them into boxes they would mark with doodles or pseudonyms so they could identify them when the vessel reached port. "They never wrote their real names on the boxes," he said.

Some whalers would take home between five and 10 boxes, he said, while one secured as many as 40 boxes of prime meat that fetches ¥20,000 (about £148) a kilo when sold legally. One crew member built a house with the profits from illicitly sold whale meat, he said. "Another used the money he earned to buy a car," he said. "They were careful to select only the best cuts, like the meat near the tail fin. I never dared challenge them."

Kujira paints an unpleasant picture of life at sea, although he is reluctant to divulge details for fear of revealing his identity.

Newcomers are badly treated by more experienced whalers, fuelled by a machismo culture that is disappearing from other parts of the fishing industry. "The treatment of junior crew has improved a lot elsewhere over the last 40 years," he said. "But the industry seems to be trapped in time."

He contradicted Japan's claims that the industry, which reportedly required government subsidies of almost $12m in 2008-09, is highly efficient. The fleet would sometimes catch more whales than necessary, he said, strip them of their most expensive parts and throw what was left overboard.

"I didn't think of the embezzlement at first. I just couldn't stand the waste. A lot of meat was being thrown away because we kept catching whales even after we'd reached our daily quota. I decided I had to tell someone what was happening."

Oddly, perhaps, for someone with his professional background, he sought help from Greenpeace. In 2008, the organisation launched a secret investigation into embezzlement by the crew of the Nisshin Maru, during which two activists, Junichi Sato and Toru Suzuki, intercepted a box containing 23kg of whale meat – worth about ¥350,000 – at a warehouse in Japan that they later presented as evidence.

After initially agreeing to act on their claims, prosecutors dropped the case and instead, Sato and Suzuki were arrested and charged with theft and trespassing.

Last week, prosecutors demanded an 18-month prison sentence for the "Tokyo Two", who were held without charge for 23 days and interrogated while strapped to chairs without their lawyers present. A ruling is expected in the next few months.

Kujira's allegations come as the International Whaling Commission [IWC] prepares to meet next week in Morocco to discuss a proposal that could end the moratorium on commercial whaling in return for whaling nations agreeing to smaller quotas. In the run up to the meeting, Japan has reverted to its preferred tactic of using aid to sway small islands and even landlocked nations to vote with it in the 88-member body.

Under the IWC moratorium, Japan is permitted to catch just under 1,000 whales – mainly minke – in the name of scientific research. Meat from the cull is sold on the open market and the profits used to fund future whaling expeditions.

Japan denies allegations of vote-buying, but has acknowledged that it invests heavily in the fishing industries of some IWC allies, and pays the expenses of delegates from poorer countries.

Kujira says Greenpeace's investigation has forced whaling crews to change their ways. "I heard from my sources that the theft of whale meat has stopped because of the media attention. But dozens of younger crewmen have left the fleet because they can no longer steal whale meat. They only joined the fleet because they knew they could make lots of money at the end of each trip. It was the only perk of a very tough job. The older whalers are just hanging on for their pensions."

The Institute of Cetacean Research has insisted that crew members take home only small quantities of whale meat as a reward for spending months working in some of the world's most inhospitable waters.

Kujira is trying to generate interest among Japan's media, which are reluctant to criticise the country's research culls while it defends itself against mounting international criticism of the annual slaughter.

Although he no longer works for the fleet, Kujira adds that he will continue to campaign behind the scenes, at great risk to his own safety, until the Japanese public learn the truth about the industry: "I dread to think what the other whalers would do to me if they knew who I was. They could do anything they wanted to me. I would be living in fear of my life."

A whale tale

The International Whaling Commission (IWC) is bitterly divided over Japan's research whaling programme.

The country slaughters about 950 mainly minke whales every year in the name of scientific research, but critics say the culls are commercial whaling in disguise, since the meat is sold on the open market.

Under a proposal submitted by IWC chairman Cristian Maquieira, Japan would be permitted to resume commercial whaling for 10 years, but would have to adhere to strict quotas "significantly lower" than current ones.

One estimate says the move could spare more than 5,000 whales over the next decade. Two other whaling nations, Iceland and Norway, would also be able to take part in the experiment. The three nations have killed 35,000 whales since the IWC ban went into effect in 1986.

They would have to agree to other conditions, such as the presence of observers on ships, DNA registers of slaughtered whales and market sampling to detect illegal whaling.

Campaigners fear the proposal could lead to a return to large-scale commercial whaling and say the IWC should be forcing whaling nations to end the culls altogether.

There are large numbers of minke whales in the north Atlantic and western north Pacific, but the proposal would also permit limited catches of fin and sei whales, both listed as endangered.

The move is under discussion and would require the support by 75% of the IWC's 88 members to pass. Despite allegations of vote buying, Japan is currently some way short of acquiring the votes it needs.