The International Fund for Animal Welfare said money raised from the sale of whale meat falls far short of the cost of running and maintaining the fleet that hunts the mammals in the Southern Ocean.
"The whaling industry has been operating in the red for more than twenty years now," Patrick Ramage of Ifaw said.
"It's the taxpayer subsidies provided by the good people of Japan that have been keeping the whaling industry afloat."
In a report issued Tuesday in Tokyo, Ifaw said whale meat consumption has been falling since a peak in the 1960s, and that Japan has around 5 000 tons stockpiled.
Japan hunts whales under a loophole in the moratorium on whaling that allows "lethal research" for scientific purposes.
But it makes no secret of the fact that meat from the slaughtered creatures ends up on dinner tables.
A Japanese fisheries agency official declined to comment, saying the agency was not aware of the Ifaw statement. But he said Japanese whaling was scientific research and was not an industry.
Japan's whaling fleet left port in December aiming to catch around 1 000 whales in the Southern Ocean, where they are being pursued by militant environmentalist group Sea Shepherd.
Japanese coastguard officers will be aboard the ships to cope with possible harassment from anti-whaling activists, the coastguard and fisheries agency officials said last year.
Sea Shepherd activists have clashed violently with whalers in the past, in exchanges that have seen stink bombs thrown at Japanese crew and water jets trained on protesters.
Last week the Australian government lodged a protest with Tokyo after a ship from the Japanese fleet entered its exclusive economic zone.
Canberra is strongly opposed to whaling and launched legal action challenging the basis of Japan's "scientific" hunt in December 2010.
IFAW, which does not take part in the sabotage missions, pushes for what Ramage on Tuesday said was a "dispassionate and logical" approach.
"Japan's dying whaling industry is being propped up by millions of dollars a year in public money," he said.
"We've encouraged [policymakers] to consider the alternative of whale watching and we've been met with an especially positive response.
"Ultimately the decision to end whaling... will be made here in Tokyo by Japanese decision makers for reasons that make sense to them."