Death comes as Beijing announced that 41 people have been diagnosed with pathogen linked to a new type of coronavirus.
A man in his 30s from Kanagawa prefecture, southwest of Tokyo, tested positive, the ministry said.
The man had been to the Chinese city of Wuhan, where there has been an outbreak of pneumonia believed to be caused by the new coronavirus strain, it said.
He reportedly returned from China to Japan with a fever and was hospitalised. He was released on Wednesday after the symptoms subsided, according to the health ministry statement.
The World Health Organization (WHO) had earlier warned that the new virus could spread and alerted hospitals worldwide.
On Monday, a Chinese woman was also ordered quarantined in Thailand after contacting the virus, authorities said.
Authorities in Asia have stepped up monitoring at airports ahead of next week’s Lunar New Year holiday when hundreds of thousands of Chinese tourists are expected to travel domestically and abroad.
On Wednesday, the US State Department also issued a health alert about travel to the Wuhan region. It referenced a Watch Level 1 Alert by the US Centers for Disease Control and Prevention urging citizens travelling in the region to avoid contact with animals, animal markets or animal products, among other precautions.
On Saturday, Chinese authorities announced that a 61-year-old man died from pneumonia, a symptom of the disease, in Wuhan.
In total, 41 cases of pneumonia have been reported in China, which preliminary lab tests cited by Chinese state media show could have been caused by a new type of coronavirus.
Coronaviruses are a large family of viruses that can lead to infections ranging from the common cold to SARS. Some of the virus types cause less serious disease, while some like the one that causes MERS, are far more severe. SARS originated in southern China in 2002 and infected more than 8,000 people in 37 countries before it was brought under control. Nearly 800 people died.
“The possibility of cases being identified in other countries was not unexpected and reinforces why WHO calls for on-going active monitoring and preparedness in other countries,” WHO said in a statement.
WHO Director-General Tedros Adhanom Ghebreyesus has been consulting international experts on the public health risks of the outbreak to decide whether an emergency meeting is needed, it said.