One of the patients was a Japanese tour bus driver in his 60s in the city of Nara who had driven two groups of Chinese tourists who had come from Wuhan earlier this month.
He was diagnosed with pneumonia on Saturday and has now been hospitalised.
Another man in his 40s who lives in Wuhan and arrived in Japan on 20 January was also confirmed to have contracted the virus, the ministry said.
The ministry said it was checking on people who had been in contact with the two new patients. The latest infections bring the total number of confirmed Japanese cases to six.
It comes as Germany’s first case of the virus was believed to have been infected by a Chinese colleague who visited his workplace.
The 33-year-old from the Starnberg area south of Munich is in isolation as a precaution, officials in Bavaria said. They said his condition was good.
The man took part in a training session at his workplace last Tuesday which also included an employee of the same company visiting from China, said Andreas Zapf, the head of Bavaria’s office for health and food safety.
The woman, who had not previously shown any symptoms, flew home on Thursday and went to a doctor after feeling ill on the flight, Mr Zapf said. She then tested positive for the new virus.
The woman lives in Shanghai, but had been visited a few days earlier by her parents, who come from the worst-affected Wuhan area.
On Monday, the German company was informed of the positive test, and informed authorities and employees.
An employee who had been at the training session came forward and said he had experienced bronchitis-like symptoms over the weekend, though they had receded and he came to work on Monday.
Authorities decided when they received positive test results on Monday evening to admit him to a hospital and put him in isolation for monitoring.
Auto parts supplier Webasto confirmed it was the company involved and said the man works at its headquarters in Stockdorf, south of Munich. It cancelled all travel to and from China for the next two weeks and said employees at Stockdorf are free to work from home this week.
The WHO said a case in Vietnam also involved human-to-human transmission outside China.
The coronavirus has infected thousands of people in China. Nearly all of the cases outside China are among people who recently arrived from there.
Additional reporting by agencies
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