A man in his 30s from Kanagawa tested positive, the ministry said. The man had visited Wuhan city where there is an outbreak of pneumonia believed to be caused by the new coronavirus strain in China.
The World Health Organisation has said the new virus could spread from human to human and has warned hospitals worldwide to be on alert.
In China, the government has reported 59 new coronavirus cases and one death with 739 people being monitored. So far there have been no reports of human-to-human transmission.