Start from November 1st, 2020, Japan allows all foreign nationals from countries/regions designated as subject to denial of permission to enter Japan, with the status of residence that have a valid re-entry permit to enter the country without a need to present a “Letter of Confirmation of Submitting Required Documentation for Re-Entry into Japan” or “Receipt of Request of Re-Entry”, that was needed to be obtained at the Japanese embassies abroad.
On top of that, the certificate of a negative test result that was conducted within 72 hours before the departure time of the flight is still necessary and needs to be presented to a quarantine officer upon arriving in Japan.
Japan’s Ministry of Foreign Affairs provides the valid format of the certificate of negative test results here. You need to have a certificate with this format filled and signed by a medical institution.
Note that, if applicants enter Japan with false documents, it will cause the revocation of the status of residence and could be subject to deportation based on Ordinance for Enforcement of the Immigration Control and Refugee Recognition Act.
Source : Japan’s Ministry of Foreign Affairs