High bids traditionally mark the year's first auction at Tokyo's Tsukiji fish market.
Even the buyer, sushi chain owner Kiyoshi Kimura, who also paid out the record price last year, said the cost was "a bit high".
The sale came amid continued warnings from environmentalists that tuna stocks are dwindling and overfished.
This year's record-breaking fish was caught off north-eastern Japan and weighed in at 222kg (489lbs), some 47kg lighter than last year's prize-winner, which fetched 56m yen.
The prices do not necessarily reflect quality or size and are more linked to publicity and setting the tone for the business year.
The auction at the market - which trades millions of dollars of products daily and is a popular tourist destination -  began at 05:00 local time.
Mr Kimura immediately carted his purchase off to a nearby branch of his Sushi Zanmai chain.
He said he wanted to "encourage Japan" with his bid.
The price works out at about $7,600 per kg ($3,500/lb).
Japan consumes more than half of the world's bluefin catch.
New figures to be released on Monday are expected to show a continued decline in Pacific bluefin stocks.
Amanda Nickson, of the Pew Environmental Group's global tuna conservation campaign, told Associated Press news agency: "Everything we're hearing is that there's no good news for the Pacific bluefin. We're seeing a very high value fish continue to be overfished."
A single bluefin tuna has sold in Japan for 155m yen ($1.7m; Â£1.05m), almost triple the record price set last year.