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ZWC_yamada 
On June 26th, we submitted a request to the Tokyo Immigration Bureau regarding foreign nationals who are currently re-entering Japan or have left the country. Currently, Japan is refusing entry to foreign nationals who have a history of staying in certain countries or regions. As a result, foreign nationals who have a residence status in Japan and have left the country with a re-entry permit are unable to return to Japan, and we have received numerous inquiries from these foreign nationals and their families. We submitted this request in response to these concerns.
Specifically, we requested the following two points: ① Allow an extension of the period for a certain duration if a person is unable to return to Japan during their departure from the country due to the COVID-19 pandemic and their residence status expires; and ② While currently, foreigners with "status or position" such as permanent residents may be allowed to enter Japan if they departed with a re-entry permit before their region became subject to entry restrictions, we requested that this special circumstance also be recognized for foreigners with other residence statuses, allowing them to enter the country.
Update: The following new operational procedures were announced on July 31, 2020.
Japanese: https://www.mofa.go.jp/mofaj/page1_000864.html
English: https://www.mofa.go.jp/ca/fna/page4e_001074.html
Those holding a valid residence status (including foreigners with "status or position" such as permanent residents) who departed Japan with a re-entry permit before the day designated for entry refusal are now permitted to re-enter Japan. However, they must obtain a "confirmation letter" from a Japanese embassy abroad before entering Japan and have a "test certificate" proving they are "negative" for COVID-19.