If you plan on leaving Japan at any point during your stay here you will need a re-entry permit (sainyukoku kyoka, 再入国許可). These are absolutely necessary, if you do not have one on you passport when you leave, you will not be allowed back in on your working visa.
The permits come in two different types; a single use and a multiple use. The single use, as the name implies, can only be used once and costs 3000 yen. The multiple use permit costs 6000 yen can be used as many times as you like and lasts for the duration of your visa. So it is worth it paying for the multiple use permit, even if you don't plan on using it more than once. If for any reason you have to head home, or if you want to go on spur of the moment trip then you can do with out spending more time and money at the immigration bureau.
When you go to get your permit you will need to take the following documents with you;
* Alien Registration Card
* Passport
You can get the permits from the Gifu branch of the Immigration Bureau. The office is easy to find, just come out of the south side (the Kano side) of Gifu JR station, and head over the road to the Nihon-Izumi (日本泉) building, check out this
map for more details (Japanese only, the red square is the immigration office). The Immigration office is on the 3rd floor, but to pay for the permit you will need to buy revenue stamps (inshi , 印紙) from the little shop on the ground floor. Go straight when you enter the building and the shop is on your right at the back; it has signs up in English.
Address岐阜県岐阜市加納清水町3-8-1日本泉ビル3階
Gifu-ken, Gifu-shi, Kano Shimizu cho 3-8-, Nihon Izumui Building, 3rd Floor
Phone Number: 058-268-7050
Once you have your stamps you are all set to get your permit. Head up to the 3rd floor and ask for the forms. Once the process has begun it doesn't take too long, but depending on how busy the office is you could have to wait a little while. Opening times for the office are 9am-12pm, 1pm-4pm Mon-Fri. This means that you will probably need to take some time off work to get it done.
That should be everything you need to know in order to get your re-entry permit, good luck!