The Institute of Cetacean Research rejects accusations that crews on Japanese whaling ships are stealing and selling whalemeat from scientific expeditions.
Two former whalers claim that whalemeat gathered on such trips is being sold to restaurants or kept for personal consumption.
The two say they fear for their lives after revealing that ships' crew members are selling the meat on the black market.
One of them claims that crew members on his whaling boat carried off about 500 - 600kg of stolen whalemeat.
But the institute, which conducts Japan's whale hunts, says crew members were given whalemeat as part of a gifting programme that has existed for 20 years.
Spokesperson Glenn Inwood says the allegations have only come out now because the trial of two Greenpeace activists charged with theft ended in Tokyo on Tuesday.
Two years ago, the two activists investigated the whistle-blowers' claims.
Greenpeace spokesperson Karli Thomas says the allegations are not just a case of political spin: the whistle-blowers have spoken out now, she says, only in order to support the activists on trial.