Re-entry to Japan
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 more details, please visit http://www.immi-moj.go.jp/newimmiact_1/en/point_3-4.html
Please also note that all students enrolled in the Graduate School of Frontier Sciences must complete the procedure when leaving Japan.
For short-term (1 day to 2 months) travel such as temporary return, submit the "Overseas Travel / Temporary Return Notification to Student Affairs Team in advance. Please note this form requires the approval of your academic advisor. For details, please talk to Student Affairs Team.
2 months or longer enrollment, research or study tour at an overseas educational or research facilities have different procedures; "travel without leave" and "travel without leave". In either case, please consult with your academic advisor first and obtain their consent. Then obtain the approval of your advisor and the department chief of your major. Be sure to submit it to the Student Affairs Team window at least one month before the desired month.