Officials in Tokyo are to investigate claims that shipping crews stole a tonne of meat from Japan's whale hunt.
Documents seen by the BBC confirm that public prosecutors will examine corruption allegations lodged by the environmental group Greenpeace.
It says crew members posted boxes of stolen whale meat to their homes.
Whaling fleet operator Kyodo Senpaku says small amounts of whale meat are routinely given to the crew as a "souvenir" at the end of the hunt.
A Fisheries Agency official said it had ordered separate internal probes by Kyodo Senpaku and the government's whale research body the Institute of Cetacean Research (ICR), which are due within a week.
ICR declined to comment on the prosecutor's case, due to its own internal investigation.
Japan catches whales in the Southern Ocean around Antarctica under a clause in international whaling regulations permitting hunting for scientific purposes.
The Tokyo District Public Prosecutor's office confirmed it would investigate 12 production workers from the whaling ship Nisshin Maru.
The workers are accused of stealing whale meat from the Southern Ocean hunt, in a criminal complaint filed by Greenpeace after it tracked 47 boxes sent from the Nisshin Maru.
The environmental group also claims that government-appointed officials at Kyodo Senpaku and ICR were aware of the theft, and that restaurants and traders buy meat directly from the whaling ship before the government officially releases it for sale.
Last week, Greenpeace revealed evidence of the alleged fraud, including a box containing 23.5kg of whale meat with an estimated value between 110,000 and 350,000 yen ($1,100 and $3,500).
The box, one of four sent by a crew member to his home, had been listed as personal baggage containing "cardboard". Instead, it contained prized "unesu" meat used to make whale bacon.
Greenpeace Japan whales campaign co-ordinator Junichi Sato said the prosecutor's investigation would show Japan's public "for the first time" how its scientific whaling programme is conducted.
"Now the Japanese public will be aware how taxpayers' money is misused on this programme," he said.
Fisheries Agency official Tsuyoshi Iwata rejected this claim, saying: "We don't believe that there is any misuse of taxpayers' money on this whale research programme."
Mr Sato called for the Japanese government to halt subsidies to the programme and suspend Kyodo Senpaku's whaling permit during the investigation.
But Mr Iwata said the government would "absolutely not" suspend any whaling permits before the investigation was complete, and all research hunts would go on as planned.
The Antarctic fleet has returned to port, but the north Pacific season opens at this time of year.
Meanwhile, police are also investigating a complaint by trucking company Seino Transportation, which accuses Greenpeace of stealing the box containing whale meat from its office in the northern city of Aomori.
Greenpeace admits it intercepted the box to prove its embezzlement claims, but says that under Japanese law, such usage does not constitute theft.
Mr Sato said he had written to Seino Transportation to apologise for taking the box.
"I have sent a letter of apology to the company headquarters," he said. "We asked the company to understand why this needed to be done."
Kyodo Senpaku collects, processes and sells whale meat for ICR, a non-profit organisation authorised by the Japanese government to carry out research whaling. It reports to the Fisheries Agency.
The company says it gives each crew member about 10kg of meat as a souvenir of the Antarctic hunt; but Greenpeace claims that the 47 packages it followed were additional to the staff gifts.