It was far lower than the highest price of last year - 193 million yen - and the first auction came while Tokyo Governor Yuriko Koike repeatedly urged its residents to refrain from non-essential and non-urgent outings in order to curb coronavirus infections.
The 208-kilogramme tuna, valued at 100,000 yen per kilogramme at the Toyosu fish market in Tokyo, was sold to wholesaler Yamayuki Group.
The fish was caught in Oma on the northern tip of Japan's main island Honshu. The area is known as one of the best tuna fishing grounds in the country.
On Monday, Koike and the governors of its three neighbouring prefectures decided to ask bars and restaurants to shorten their business hours to rein in a third wave of the Covid-19 pandemic.
The Toyosu fish market opened in October 2018 after the famed Tsukiji market closed after 83 years of business.
Tsukiji was one of Japan's top tourist attractions and was used by top sushi chefs and ordinary grocery stores alike. The first auction of the year attracted big fish spenders who would pay top dollar of the biggest and best fish.
Japan is the biggest consumer of the torpedo-shaped bluefin tuna and the national and international demand for the fish has lead to overfishing of the species. Experts have warned of its extinction as stocks of the Pacific bluefin dropped by 96 percent of pre-industrial levels.
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