He works as a bus driver, and had driven two groups of Chinese tourists from Wuhan, the
epicentre of the 2019-nCOV outbreak, this month.
The trips were from Jan 8 to 11, and from Jan 12 to 16.
The man had first developed symptoms of the common cold on Jan 14. He saw the doctor three days later, but no abnormalities were found.
His condition worsened on Jan 22, developing joint aches and pains. He was hospitalised on Jan 25. The infection of the novel coronavirus was confirmed on Tuesday.
Dr Hitoshi Oshitani, an infectious diseases expert at Tohoku University, told public broadcaster NHK that person-to-person infections can be expected in Japan.
As this would be difficult to contain given the situation in China, he called for countermeasures in anticipation of the virus further spreading domestically.
The other confirmed case on Tuesday is a Wuhan man in his 40s who has been warded in Aichi prefecture.
The development comes as Japan
will land a chartered flight on Tuesday night in Wuhan which is under lockdown to stem the spread of the virus that has killed 106 and infected over 4,500 people.
The charter plane, operated by All Nippon Airways (ANA), will deliver masks and protective suits to Wuhan.