Since July 9th 2012, you are no longer required to apply for a re-entry permit if you hold a valid Passport and Residence Card and will return to Japan within 1 year from your departure date.
All you need to do is to fill out the embarkation/disembarkation card for re-entrants and remember to check off the box where it says “departure with special re-entry permission”. You must also be sure to present your residence card upon exiting and re-entering.
In case you plan to leave for more than 1 year, you would need to apply for a re-entry permit at the immigration bureau in order to maintain your long term visa and resident registration status upon your return.