From Friday, Japan will also require on-arrival virus tests for passengers from China, but that will not apply to travellers from Hong Kong and Macau.
Hong Kong had followed a version of China’s zero-COVID policy and imposed some of the strictest travel curbs in the world during the pandemic, which left the business hub isolated for more than two years.
The city only began lifting restrictions recently, ending mandatory hotel quarantine for all arrivals in September.
Since then, travel has surged as Hong Kongers clamour to take holidays and visit loved ones overseas.
Japan, which lifted its own ban on foreign arrivals in October, has also seen a major spike in travel.
In May this year, just 700 Hong Kong arrivals were recorded at airports in Japan. By November, that number leapt to 83,000.