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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 reapply for a new visa.
This information is from the website of Immigration Bureau of Japan.
For more details, please visit http://www.immi-moj.go.jp/newimmiact_1/en/point_3-4.html