Note: The Alien Registration system was abolished in summer 2012 and has been replaced by a new Residency system. Please view the following Ministry of Justice pamphlet for more details: http://www.immi-moj.go.jp/newimmiact_1/pdf/NewResidencyManagementSystem-%28EN%29.pdf
Re-entry permits are no longer necessary if you will be out of Japan for less than one year, either for holders of the old Alien Registration Card or the new Residence Card.
However, you will still need to fill out a form when you leave the country at immigration, this will be stapled onto your passport. When you return to Japan immigration officials will tear off the main part of the form so don’t dis attach it from your passport!