From July 9, 2012, you do not need to get a re-entry permit to go out of Japan temporarily, keeping your current visa status.
This new re-entry system is only for short-term overseas travel and you need to be back to Japan within one year after you leave Japan. If you fail to do so, you will automatically lose your visa status. There is NO excemption for one-year rule even in case of accidents.
If you want to be outside Japan over one-year or if you want to avoid trouble caused by accidental long stay overseas, you can apply for re-entry permit.
Just as before, there are 1) single re-entry permit (it costs 3,000 yen) and 2) multiple re-entry permit (it costs 6,000 yen).
You may get the application form the download page.