"We have asked airlines not to accept new bookings for a month from December 1," a ministry official told AFP, adding that existing bookings were not affected.
These new restrictions come as a second case of the Omicron variant of Covid-19 was confirmed in the Archipelago on Wednesday.
The Japanese government said it was a traveler who arrived from Peru last week.
The first case, announced Tuesday, involved a man from Namibia.
Japan had already announced Monday the closure of its borders to all foreign visitors, just three weeks after relaxing some restrictions to allow the entry of business travelers, students and foreign interns.
The new restrictions therefore only apply to Japanese citizens and foreign residents in Japan, the only ones allowed to enter Japanese soil.
The government also decided on Tuesday to close its borders to all foreign nationals from ten southern African countries, including South Africa, where the Omicron variant was first identified.
Japan has been relatively spared from the pandemic, with some 18,350 dead since early 2020. It has also avoided strict containment measures, unlike many other countries.
After a slow start, the national immunization campaign has gained momentum and nearly 77% of the country's population has now received two injections.
The administration of a third dose began Wednesday for people fully vaccinated for at least eight months.
© 2021 AFP