It means the country will restore border controls it had only eased earlier this month for short-term business visitors, foreign students and workers.
Prime minister Fumio Kishida told Sky News the country is responding to the Omicron strain, which was declared a "variant of concern" by the World Health Organization, with a "strong sense of urgency".
Over the weekend, Japan tightened entry restrictions for people arriving from South Africa and eight other countries, requiring them to undergo a 10-day quarantine period.
The move comes as other global governments reintroduce lockdown measures in a bid to curb the spread of the new variant.
