At a market in central Tokyo this week, a bluefin tuna the size of five Japanese men fetched £250,000 at auction. It was partly a show of New Year ostentation but proof, too, that Japan has not lost its appetite for an endangered species.

Whales, however, are no longer so popular. At refrigerated stores across the country, thousands of tonnes of whalemeat lies unsold.

The Japanese Dolphin and Whale Action Network said the country's whalemeat stockpile exceeded 6,000 tonnes last August, a record high.

It seems that just as Japan's whaling fleet is beginning its annual "scientific" kill of just under 1,000 whales – mainly minke – the nation's consumers are voting with their chopsticks.

The attraction of bluefin tuna is still too great to resist, despite dangerously low global stocks; whalemeat, by contrast, lost its allure long ago.

It has been claimed that substandard freezing methods on whaling ships, combined with the high price of the meat, have led to the decline in popularity, and the days when whalemeat formed a regular part of school lunches is long gone.

Annual per capita consumption is now equivalent to just four thin slices a year. "There is no demand, and there is no consumption," said Wakao Hanaoka, ocean campaigner for Greenpeace Japan.

But tuna's popularity in Japan, where about 600,000 tonnes is eaten annually – mainly raw as sushi or sashimi – shows no signs of abating.

Top-grade otoro, the fattiest cut, can sell for as much as 2,000 yen (£16) a piece at exclusive Tokyo restaurants. Japan consumes about 80% of Pacific and Atlantic bluefin tuna and has been accused of stifling global attempts to curtail fishing quotas or ban the trade altogether.

The WWF has warned that if fishing continues at current rates, the Atlantic bluefin will be "functionally extinct" in three years.

But this did not appear to be a concern at Tuesday's auction at Tsukiji market in Tokyo. The price paid for the 342kg (53 stone) tuna easily beat the previous record, set exactly a decade ago, when a 202kg fish fetched £155,000.

Market officials are accustomed to seeing prices rise during the year's opening auction at Tsukiji, the world's biggest fish market, but the new record was still unexpected.

"It was an exceptionally large fish," said Tsukiji spokesman Yutaka Hasegawa. "But we were all surprised by the price."

The fish, one of more than 500 tuna shipped in from around the world for the first dawn auction of the year, will be divided between two sushi restaurants – one in Tokyo, the other in Hong Kong – which joined forces to bid.

"The custom of eating raw fish is spreading throughout the world, so that it's no longer an era where Japan is consuming all of the limited supply of tuna," an auction manager said.

In Japan, many consumers have yet to fully understand the consequences of overfishing.

"They go to the supermarket and see tuna lined up alongside lots of other varieties of seafood, all similarly priced, and are fooled into thinking everything is available in abundance," said Hanaoka.

"But it is not possible for the Japanese to continue to eat tuna at this rate."

Last year Hideyuki Komatsu, a Japanese champion of sustainable fishing, suggested that if whale could be frozen better, it should replace tuna on the menu.

He believes that certain species of whale, notably the minke, are abundant enough to be killed sustainably. He said: "While the minke whale has a green light above it, the fin whale has a yellow light. But a red light is flashing over the bluefin tuna."