Japan will send a chartered flight to the central Chinese city of Wuhan later in the day to repatriate about 200 of its citizens, the government says.
The government will also send doctors, nurses and quarantine officers so that those Japanese citizens can undergo checkups on a plane, according to the health ministry.
The aircraft is scheduled to come back to Japan on Wednesday, Foreign Minister Toshimitsu Motegi says.
Since a total of 650 Japanese in Wuhan wish to return, the government will send more flights to take them home, Mr Motegi says.
China and countries around the world are scrambling to contain the spread of the coronavirus that has killed at least 106 people and infected more than 4,500.
Germany has reported its first case of the virus, as the U.S., and Canada upgraded travel warnings to advise their citizens to avoid all non-essential travel to China.
More than 56 million people in almost 20 Chinese cities – including Wuhan, capital of Hubei Province and the epicentre of the virus – have been prevented from travelling, in an attempt to curb the spread of the virus during the Lunar New Year or Spring Festival, traditionally China’s busiest travel season.
The director-general of the World Health Organisation (WHO) is currently in China.
The agency has acknowledged that the respiratory illness is an emergency in China but said last week that it was too early to declare the outbreak a public health emergency of international concern.
It has described the global risk from the virus as high.