Can I leave japan with my visa ?

I'm Indonesian, I have a single entry visa, and my type of visa is student visa for 6 month. But at this December I want to leave japan to Philippine. Do I need the re-entry permission ? Or can I leave and go back to japan wherever I want ?

You can leave and come back as long as it is within the validity of your residency. No special permit is needed.

Actually, yes, you quite literally need a "special" permit. ;) It's all explained here:

http://www.immi-moj.go.jp/english/tetuduki/zairyuu/specialre-entryperm...

Only the special re-entry pernit right ? Like a simple paper which is for disembarkation and embarjation right ? But no need for me to apply re-entry right ? Even tho single entry student type ?

Actually, yes, you quite literally need a "special" permit. ;)

Yes, that is true. Practically speaking, however, its not something you need to apply for in advance, but a box that you check on your exit form as you go through exit immigration. In many cases, the immigration officer will check the box for you if you don't indicate that you are exiting Japan for good, so in effect it is virtually automatic. Here's a more detailed link on the process:

http://www.immi-moj.go.jp/newimmiact_1/en/point_3-4.html

You need to apply for a re-entry permit. If you don't then they will take your Foreigner Registration Card at the airport and you will have to get a new visa in order to re-enter.

http://www.immi-moj.go.jp/english/tetuduki/kanri/shyorui/06.html

You need to take your passport, registration card, the fee, and one of the application forms on that site to the Immigration Office that serves your registered address.

You need to apply for a re-entry permit.

No, the system changed in 2011 and you no longer need a re-entry permit if you spend less than a year outside Japan.

Single Entry Visa:
This is a piece of paper/sticker n your passport that give you permission to enter Japan as per your Visa Status (Student Visa). Normally this is issued and valid for 90days from the issued that. This mean you must used it within that 90days to enter Japan and only use it once. A multiple entry Visa will let you enter Japan as many time ad you can within the Visa period(normslly expire longer tha single entry).This Visa will be void/cancel/finished obce you used it to enter Japan (single entry).

Landing Permission & Zairyu/Resident Card:
Once you entered Japan with above mentioned Visa, at the airport the Immigration will stamp your Visa page on the pasport to cancel it *USED* (in case of single entry)
and anothet stamp landing permission that is correspind to your Visa status with period of stays (in your case Student Visa starting from your entry date upto 6months) also you will received Zairyu/Resident Card which also show your Student Visa status with expiry date.

Re-entry after July 2011(new immigration law)
If you plan to go out and return Japan in less than one year, just fill in the special re-entry disembarkation card at the airport and make sure you check the re-entry box on the card. That is all no need for application form/fees as before July 2011. One stay outside Japan more than one year (return before resident status expired ) will require application and fees.

Visa, Visa Status(Resident Status), Landing Permission/Status, Zairyu/Resident Card, Special Re-entry Permit