It was bought by Kiyoshi Kimura, president of Sushi Zanmai, a major sushi restaurant chain.
Bidding stopped at a whopping 333.6 million yen for the enormous 278-kilogramme (612-pound) fish - an endangered species - that was caught off Japan's northern coast.
The fish's price tag is the equivalent of almost 70kg of gold or a three-bed apartment in Manhattan, but Kiyoshi Kimura believes it's worth every cent as he's eager to serve his clients.
Saturday's event was the first New Year auction of the Toyosu market, after the famed Tsukiji fish market shut last year to provide temporary parking for the Tokyo 2020 Summer Olympics.
"The quality of the tuna I bought is the best", he stated as quoted by Japanese broadcaster NHK, adding that the high prices surprised him.
The winning sum for the prized and threatened species at the auction was more than double the previous record from the annual New Year auction, set in 2013. "I was able to buy a delicious, super fresh tuna", the sushi restaurant chain owner proudly told reporters.
Last year's auction was the last at Tsukiji before the market shifted to a new facility on a former gas plant site on Tokyo Bay.More news: U.S. crude oil inventories decrease last week: API
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The previous site at Tsukiji opened in 1935 and became the world's biggest fish market and a popular tourist attraction.
At 5.10 am, handbells rang to signal the auction was underway and the air filled with the sound of auctioneers yelling prices at buyers, who raised fingers to indicate interest.
Mr Kimura has been the highest bidder at the new year auction for seven of the past eight years.
Japan is the biggest consumer of bluefin tuna, leading to the overfishing of the species, with some experts warning that it faces extinction.
"Finally, the first New Year auction was held at Toyosu market", said Yoshihiko Otaki, a market official.
After the auction, the fish was taken to one of Sushizanmai's branches located in the old market of Tsukiji.
The relocation was a lengthy and controversial process.