Japan's health ministry said a man who had visited the central Chinese city of Wuhan, the apparent epicentre of the outbreak, was hospitalised on January 10, four days after his return to Japan. He reported a persistent fever.
Tests on the patient, who was released from hospital on Wednesday, confirmed he was infected with the new virus.
"This is the first domestic discovery of a pneumonia case related to the new coronavirus," the ministry said in a statement.
"We will continue active epidemiological research while also coordinating efforts with the World Health Organization and related agencies to conduct a risk assessment."
The outbreak has killed one person so far, with 41 patients reported in Wuhan.
The outbreak has caused alarm because the new virus is from the same family as the pathogen that causes SARS (Severe Acute Respiratory Syndrome), which killed 349 people in mainland China and 299 in Hong Kong in 2002 and 2003.
Authorities in Wuhan said a seafood market was the centre of the outbreak. It was closed on January 1.
Japanese authorities said the man had not visited the market and that it was possible he had been in contact with a person infected with the virus while in Wuhan.
Outbreak in Japan 'unlikely'
Health ministry official Eiji Hinoshita told reporters that the risk of the disease spreading from the patient was considered low, with careful checks done on those who had been in close contact with him.
"At this point, we feel it is unlikely this will lead to a dramatic outbreak," he said, adding that the patient was no longer suffering a fever and was recuperating at home.
Officials declined to give further information on the man, including his nationality, citing privacy concerns.
Local media said the patient was a Chinese national in his 30s living in Kanagawa, just southwest of Tokyo.
Public broadcaster NHK said he had already recovered and was resting at home, as quarantine officials at Tokyo's Narita airport boosted health checks on all travellers.
The health ministry urged people who develop a cough or fever after visiting Wuhan to wear a surgical mask and "swiftly visit a medical institution".
Hinoshita said Japan would need to be on guard ahead of the Lunar New Year, a popular travel period in China.
"It is expected that Japan will see many visitors from China," he said.
It is not yet clear whether the mystery virus can be transmitted between humans, but on Wednesday authorities said it was possible it had spread inside a family.
The woman diagnosed in Thailand, who is in a stable condition, also said she had not visited the Wuhan seafood market.
And WHO doctor Maria Van Kerkhove on Tuesday said she "wouldn't be surprised if there was some limited human-to-human transmission, especially among families who have close contact with one another".
Hong Kong authorities on Tuesday said several dozen people had been hospitalised with fever or respiratory symptoms after travelling to Wuhan, but no cases of the new virus have so far been confirmed.