TOKYO, Japan (CNN) -- Greenpeace filed a criminal complaint with Japanese prosecutors Thursday, accusing whaling-ship crew members of stealing whale meat from a hunting trip.
The environmental group said "large-scale embezzlement" was allowed as an "open secret" by the Institute of Cetacean Research in Japan. The body oversees Japanese whale hunts, which are done in the name of "scientific" research.
The institute has previously accused Greenpeace and other organizations of "harassment" for interfering with Japanese whaling voyages.
The environmental group said that 12 members of a one whaling ship sent out at least 47 boxes of whale meat after they returned to a Tokyo port.
At the press conference, Greenpeace showed one box that it said contained about 52 pounds (23.5 kilograms) of salted whale belly meat worth up to $3,000.
The Japanese Fisheries Agency said that there is a long-standing custom of giving small amounts of whale meat to crew members as a "souvenir." It said it will investigate to determine whether embezzlement is taking place.
Junichi Hoshikawa, the executive director of Greenpeace in Japan, said at a press conference that the embezzlement of whale meat "will hurt Japan's credibility and trust, which is already shaky under so-called 'scientific' research whaling."
In the early 1980s, the International Whaling Commission determined that there should be a moratorium on commercial whale hunting. Whaling is allowed under international law when done for scientific reasons, which Japan cites as the legal basis for its hunts.
The country's annual hunt kills up to 1,000 whales a year. Many in the international community say such hunts amount to needless slaughter. Critics say that Japan's research is actually a pretext for retrieving whale meat to be sold in markets and restaurants.
Greenpeace and other environmental groups have waged a long battle against Japan's whaling activities.
This year's 101-day hunt was dogged by Greenpeace and Sea Shepherd Conservation Society vessels. The Japanese whaling fleet caught 551 minke whales -- more than a third less than its goal of 850.
"This year's mission was disrupted intensively by Greenpeace and Sea Shepherd, who use violent means for disturbance," Hajime Ishikawa, the head of Japan's whaling mission, said last month.
"Putting aside our own safety, their action put their own lives in danger ... Therefore, we had to stop whaling a total of 31 days."
The Web site for Sea Shepherd, a hardline conservation group, called the operation a "huge success."
Greenpeace also claimed success interfering in the Japanese whale hunt.
"Greenpeace played a significant part in nearly halving the amount of whales killed this season," said Junichi Sato, Greenpeace Japan's whales campaigner. "However, 551 whales is still over a hundred more than Japan took three years ago ... This blatantly commercial whale hunt must end immediately."
In March, Japanese whalers and anti-whaling activists clashed in waters near Antarctica.
Sea Shepherd founder Capt. Paul Watson told CNN that two of his crew members were injured when crew members on the Japanese ship Nisshin Maru threw flash grenades aboard his ship, the Steve Irwin.
Watson also said he took a bullet to the chest while wearing a Kevlar vest. "We don't know where that bullet came from," he told CNN.
Japan's Institute of Cetacean Research, which runs the Japanese whaling ships, denied firing any shots.
"No one shot Paul Watson. His claim that we shot at him and he has the bullet that was stopped by his bullet-proof vest is more fiction for articles by the Australian media," said Minoru Morimoto, the director general of the institute, in a news release on its Web site.
The institute said it threw seven "sound balls," which it described as "harmless" explosive devices, after people aboard the Sea Shepherd threw bottles of butyric acid -- an acid found in rotten butter -- at the Nisshin Maru.
The Japanese Coast Guard had also given "clear and loud warnings to the Sea Shepherd vessel during two passes," the institute said. It did not describe the type of warnings.
The institute said it was "disappointed that more serious means were required today for defending its research vessels in the Antarctic."
The International Whaling Commission will meet in Chile next month to discuss reaching an agreement on whale conservation rules.
Japan's Ministry of Foreign Affairs and its Fisheries Agency have lobbied a dozen members of the whaling commission, making their case to officials from Angola, Eritrea, the Republic of the Congo, Guinea, Ghana, Malawi, Tanzania, Palau, Micronesia, Cambodia, Laos and Vanuatu.
CNN's Yoko Wakatsuki contributed to this report.