Re-entry permit

Residents of Japan who are not Japanese citizens may depart from Japan and re-enter without their status of residence lapsing, provided they have re-entry permission and adhere to the rules thereof.

There are two basic types of re-entry permission^[1]:


Type	Validity	Process	Cost
Re-entry permit (single or multiple)	5 years (6 years for special permanent residents) from date of issue, or until status of residence expires, or until usage is made (in the case of single re-entry permit); extendable for up to 1 year in exceptional circumstances.	apply for and obtain at your Regional Immigration Bureau. To use: inform Immigration of intent to return to Japan on Embarkation Disembarkation Card (ED Card) when departing Japan	¥3,000 (single)or ¥6,000 (multiple)
Special re-entry permit	1 year from date of departure (or until expiration of status of residence, if that is sooner); not extendable	inform Immigration of intent to return to Japan on Embarkation Disembarkation Card (ED Card) when departing Japan	Free

This article will first cover the special re-entry permit, due to its simplicity, and then examine the re-entry permit and associated procedures.

Special re-entry permits

Residents of Japan who are not Japanese citizens can gain special re-entry permission in a simple, routine and free procedure on departure from Japan (provided they are not subject to any detention orders or other cases rendering them ineligible).

Special re-entry permits are valid until the earlier of the two:

One year from departure (or two years in the case of special permanent residents)
Until the expiration of the period of stay

Permission should be sought on departure from Japan by stating the intent to return to Japan. This is done on the Embarkation Disembarkation Card (ED card), which has two boxes (image provided in link):

I am leaving Japan temporarily and will return.
I do not plan to re-enter Japan while my re-entry permit is valid.

Those who select (1) will have opted in to the special re-entry permit (unless they already have a valid re-entry permit), provided Immigration are satisfied with the individual’s credentials, etc.

Special re-entry permits can not be extended. If an individual does not return to Japan within the validity period of the special re-entry permit, they will lose their status of residency when the special re-entry permit expires.

Re-entry permits

Ordinarily, a re-entry permit is valid for 5 years (6 years for special permanent residents), or until an individual’s status of residency expires. This may be extended by up to 1 year (for a maximum duration of 6 years) if exceptional circumstances make a timely return to Japan impractical.

Applicants can apply for a single (¥3,000) or multiple (¥6,000) re-entry permit at their Regional Immigration Bureau in Japan. It is not possible to obtain a re-entry permit from a Japanese embassy or consulate after departure from Japan.

The bilingual Re-Entry Permit Application Form (再入国許可申請書; Sai Nyukoku Kyoka Shinseisho) is available online (via the MOJ link provided) in both PDF and Excel formats, and hard copies are available at Regional Immigration Bureaus. The associated fee payment slip is also available in PDF and Excel formats via the above MOJ link, with hard copies available at Regional Immigration Bureaus.

Re-entry permits for successful applicants will ordinarily be granted on the day of application, and payment must be made in revenue stamps which are ordinarily available from a convenience store or other facility nearby the Regional Immigration Bureau.

The MOJ page linked above provides further details about applications, including the case of application via proxy.

There are no restrictions on applying for a new re-entry permit while a current one is still valid.

Re-entry permit validity and passport validity

The re-entry permit itself will remain valid until the uses are up or it reaches its expiration date, irrespective of passport validity.

Should your passport expire while the re-entry permit is valid, you have two options:

carry both the old passport with re-entry permission and the new, valid passport when you re-enter Japan
transfer the re-entry permission from your old passport to the new one by submitting an “Application for transfer of endorsements” (証印転記願出書 shouin tenki negaide sho) to your Regional Immigration Bureau, bringing in both the new and old passports. Information on this is published by the MOJ (Question 14, Japanese).

Certificate of re-entry permission in case of lost passport, etc

Those who have received a re-entry permit (including a special re-entry permit) and lost their passport or residence card while leaving Japan, are able to re-enter Japan. If you do not have documents that prove that you have been granted a re-entry permit, you can obtain a certificate of the re-entry permit expiration date. The procedure is to apply to the Regional Immigration Bureau through an agent (relative who lives with the individual or a person with a valid letter of proxy).

Extension of re-entry permit

It is not possible to obtain re-entry permit at an Embassy or Consulate-General after departure from Japan. However, if a foreign national who departs Japan after acquiring a re-entry permit and is unable to return to Japan due to unavoidable reason, such as illness, travel interruption, or continuation of studies, can apply, even after the period of validity of the re-entry permit expires, for an extension of the re-entry permit's period of validity at the Japanese Embassy or Consulate.

Source: MOFA

Considerations

Many long-term residents of Japan feel that a re-entry permit is a good ‘insurance policy’ against losing their status of residence via an extended absence from Japan.
A new re-entry permit can be applied for while a current one is still valid
Although the re-entry permit application form asks for details such as 'expected dates of travel', anecdotal evidence suggests that permits can be granted when such information is not known and not filled in

Resources

Immigration Services Agency page on re-entry permission
Immigration Services Agency Q&A page: in particular, Procedures for temporary departure (Q54-Q61)
The legislation underpinning re-entry permission can be found through the Japaneselawtranslation link. The legislation is entitled 出入国管理及び難民認定法（昭和二十六年政令第三百十九号）/ Immigration Control and Refugee Recognition Act (Cabinet Order No. 319 of 1951), and the relevant sections are Article 26 (Re-entry Permission) and Article 26-2 (Special Re-entry Permission).

Notes

↑ For convenience, the word "permit" has been used below for both types of permission, although in the case of special, or "deemed," re-entry permission (minashi sainyuukoku kyoka みなし再入国許可), no permit is actually applied for or received. Rather, a foreign resident who at the port of departure presents an embarkation-disembarkation (ED) card with the appropriate box checked is processed as having received permission to reenter the country for up to one year.

[1] For convenience, the word "permit" has been used below for both types of permission, although in the case of special, or "deemed," re-entry permission (minashi sainyuukoku kyoka みなし再入国許可), no permit is actually applied for or received. Rather, a foreign resident who at the port of departure presents an embarkation-disembarkation (ED) card with the appropriate box checked is processed as having received permission to reenter the country for up to one year.

[1]