Foreigners in possession of a valid passport and resident card who will be reentering Japan within 1 year of their departure to continue their activities in Japan will, in principle, not be required to apply for a re-entry permit. (This is called a special re-entry permit.) When you leave Japan, be sure to present your residence card and tick the column indicating your intention of departure by the Special Re-entry Permit System on an ED (Embarkation / Disembarkation) card for Special Re-entry Permit.
Foreigners who have departed from Japan on a special re-entry permit will not be able to extend that permit while abroad. Please note that such foreigners will lose their resident status if they fail to re-enter Japan within 1 year of their departure. If your period of stay expires within 1 year after your departure, please ensure that you re-enter Japan before the expiration of your period of stay, otherwise you will have to apply for a new visa.
* This information is from the website of the Immigration Services Agency of Japan. For details, please refer to the following site. https://www.moj.go.jp/isa/applications/procedures/minashisainyukoku_00001.html
* Special re-entry ED card
https://www.moj.go.jp/isa/publications/materials/re-ed_index.html
https://www.moj.go.jp/isa/content/930002122.pdf
All students enrolled in the Graduate School of Frontier Sciences must complete the procedure when leaving Japan. For details of the procedure, please refer to "Procedures for Traveling Abroad".