The 276 kilogram bluefin tuna – caught off Japan's northern region of Aomori – sold for 6.07 million yen ($55 706), an official at the Tsukiji fish market said.
The final price was a record for Japan and nearly two million yen more than the previous year, he added.
A Hong Kong-based sushi restaurant chain owner made the highest bid, local media reported although the fish market official was unable to confirm details about the buyer.
Prices of tuna caught overseas were on average 20 to 30 percent higher than the previous year as imports of cultured tuna from Mediterranean countries including Croatia and Spain have dropped sharply, Kyodo News said.
The record prices come amid a decline in tuna supply due to tighter international controls on the catch for bluefin tuna.
Japan, which eats a quarter of the world's tuna, is moving towards limiting bluefin tuna fishing in its own waters in a bid to help protect the species from extinction.
The Tsukiji market sold a total of 2 904 bluefin tuna or 176.6 tonnes Saturday, down from 3 268 or 178.6 tonnes at last year's opening auction.
Japan reached an agreement in January 2007 with the European Union to slash its tuna quotas by more than 20 percent.
This was in line with a decision by an international commission in November 2006 to cut the total hunt of bluefin tuna in the Atlantic Ocean and Mediterranean by 20 percent by 2010.
The 43-member International Commission for the Conservation of Atlantic Tuna approved a quota of 28 500 tonnes for 2008 and 25 500 by 2010 but failed to set national quotas.
Environmentalists have warned that tuna face eventual extinction if fishing continues at current rates to feed a worldwide fad for Japanese food such as sushi.