On October 30, 2020, the Government of Japan announced new procedures for re-entry from November 1.
Foreign national residences who re-enter Japan after 1 November 2020, do not need to obtain the "Receipt for request of re-entry". Foreign nationals who stayed in the countries / regions designated as subject to denial of landing within 14 days before re-entering Japan, need to bring the Certificate of Testing for COVID-19 in the country/region of stay to prove a negative test result having undergone a test for COVID-19 within 72 hours prior to departure from the country/region of stay.
The following 1) and 2) must be done by everyone.
Those who enter Japan from a country / region subject to entry refusal must also do 3) and 4).
[What everyone has to do]
1) Please understand and comply with the contents of border measures by the Japanese government. (Prohibition of use of public transportation after entering Japan, etc.). Please check the current border control measures yourself.
2) As in the past, you will also need to obtain a Special Re-entry Permission or Re-entry Permission. (Click here for more detail.)
* We strongly recommend if your Status of Residence has less than three months remaining, that you extend your status before leaving Japan. For more details about how to apply for an extension of Status of Residence, please refer to this question. Moreover, for information on taking classes from your home country and other remote areas, please check here.
[Must be done only by students entering from the country / region subject to entry refusal]
3) Be sure to obtain a negative COVID-19 test result conducted within 72 hours before leaving the country/region of stay.
4) Upon arrival in Japan, you will be inspected for new coronavirus infections at a quarantine station in airport.
*Reference for more details: Ministry of Justice homepage regarding Request of intention to re-enter Japan for foreign nationals with status of residence currently residing in Japan.
http://www.moj.go.jp/nyuukokukanri/kouhou/nyuukokukanri07_00245.html