You may leave Japan and come back again on your working holiday visa so long as you do so while your visa is still valid. Your visa doesn’t “pause” while you are gone so any time spent out of Japan is time lost.
If you see/hear information about “re-entry permits”, just ignore it. The system was changed in 2012 and they are no longer necessary.
All foreign residents of Japan need to complete a departure card. These are located on desks at airports between security (where your bags are scanned) and passport control (where immigration staff in booths stamp your passport out).
All you need to do is select the “I am leaving temporarily” box and you’ll be OK!
Important note: Your visa doesn’t “pause” while you are gone. The expiry date of your visa remains the same and you must enter Japan again while your visa is current. If your visa is renewable and expiring before your intended return date, ensure that you have fully completed the visa extension process. (Info on that in the point above).
See example Departure Card below:
IMPORTANT: If for some reason the immigration staff don’t give you your Resident Card back SAY SOMETHING! That’ll be your last chance if they’re about to accidentally cancel your visa!
• Even if you don’t intend on returning to Japan we recommend that you tick that you are in case you change your mind later. It also means you can keep your resident card as a souvenir. If you tick that you’re leaving permanently it will be taken off you. If you tick that you are coming back Japan but don’t, it’s no problem. Your visa will simply expire with no negative ramifications.
Australians: Although you can get a total of 1.5 years on your WHV, it’s only valid for 6-months at a time. You must return to Japan to extend it before the current 6-month period you’re on expires. You cannot extend the visa from outside Japan.
The “Arrival” part of the above Departure Card will have been stapled into your passport. Ensure that is completed and when you land you don’t have to wait with all the tourists in the long lines of foreigners. You can use the Permanent Residency Holder / Special Re-Entry Permit Holder line which usually only has one or two people in it! Lucky!!