The entrepreneur told reporters after the auction that he was “surprised at the price”, AFP reported.
“I’d thought we would be able to buy a little cheaper, but the price soared before you knew it,” he said.
Mr Kimura paid 56.5 million yen for a bluefin tuna in 2012 and 155 million yen in 2013 – setting record prices both times.
In 2019 he bought a bluefin tuna with 333.6 million yen ($2.1m; £1.6m) – another historic price.
Despite telling reporters at the time that he thought he “did too much”, however, Mr Kimura has now gone on to break his own record again.
The first auction at Tokyo’s Toyosu fish market typically sees fish selling for exorbitant prices.
Last year, the first tuna at the auction was bought for 207 million yen by Onodera Group, another food company that owns a sushi chain. It said that the fish would be served at its restaurants across the country.
The frenetic energy at fish markets during such pre-dawn auctions has become a popular tourist attraction in Tokyo. Monday’s auction, which started at around 05:00 local time (20:00 GMT), was no exception.
The million-dollar tuna was sliced up for customers at Kimura’s sushi restaurants shortly after it was auctioned off.
“I feel like I’ve begun the year in a good way after eating something so auspicious as the year starts,” one of the customers at Mr Kimura’s restaurant told AFP.