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apfseditor 
On June 26th, we submitted a request to the Tokyo Immigration Bureau regarding foreigners who are re-entering or leaving the country. Currently, Japan refuses entry to foreigners who have stayed in certain countries or regions. As a result, foreigners with resident status in Japan who have left the country with re-entry permission are unable to return to Japan, and we have received many inquiries from foreigners themselves and their families. We submitted a request to express these concerns.
Specifically, they requested that 1) an extension of the period be granted for a certain period of time in cases where a person is unable to return to Japan during re-entry or departure due to the COVID-19 pandemic and the expiration date of their residence status has passed; 2) in cases where a person left Japan with re-entry permission before their area became subject to landing refusal, currently foreigners based on their "status or position" such as permanent resident may be able to enter the country if special circumstances are determined to exist depending on the date and area of departure, but that these special circumstances be recognized and foreigners with other residence statuses be allowed to enter the country as well.
Addendum: The following new operations 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 with a status of residence (other than foreigners with "status or position" such as permanent residents) who left Japan with re-entry permission by the day before the entry refusal date are now able to re-enter Japan. However, they must obtain a "Confirmation Letter" from a Japanese embassy overseas before entering Japan, and a "Test Proof" that they are "negative" for the new coronavirus.