"I bought a good tuna", the self-styled "Tuna King" said after the auction.
Especially at the first auction of the new year, wholesalers and sushi tycoons have been known to pay eye-watering prices for the biggest and best fish.
The winning bid for the prized but threatened species at the predawn auction Saturday was more than double the 2013 annual New Year auction.
A 278-kilogram bluefin tuna sold for 333.6 million yen ($3.1 million) at a Tokyo fish market Saturday.
Kimura has often won the annual auction in the past. But he added: "The quality of the tuna I bought is the best".
Bluefin tuna normally sells for up to $40 a pound, but the price steeply increases by the year's end and reaches its highs for prized catches in Northern Japan.
He told Japanese TV he was surprised by how much the fish went for at the early morning auction.
Tsukiji - the world's biggest fish market and a popular tourist attraction in an area packed with restaurants and shops - moved in October to Toyosu, a former gas plant a bit further east.
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The Japanese are the biggest consumer of bluefin tuna and experts warn the species could become extinct because of overfishing.
But the Japanese government, together with other countries, is backing plans to rebuild Pacific bluefin stocks of the fish, which is now depleted by 96 percent from their pre-industrial levels.
The move to Toyosu was repeatedly delayed because of concerns over soil contamination.
The new market at Toyosu has already opened a balcony allowing visitors to witness the organised pre-dawn chaos in an attempt to attract tourists who previously visited Tsukiji.
The Tokyo metropolitan government decided in 2001 to relocate the aging Tsukiji market to Toyosu, but the initial plan to open the new market in 2016 was pushed back following the discovery of pollutants and subsequent decontamination work.
In contrast, the new market, located around two kilometres to the east at Toyosu, boasts state-of-the-art refrigeration facilities and is almost twice as big again as Tsukiji.
Tsukiji is due to be redeveloped, though for now it's being turned into a parking lot for the 2020 Tokyo Olympics.