My understanding of the guidelines for applying for permanent residence visa status in Japan is that unless you are the child or spouse of a Japanese national then you will need to:
- Fill in forms (naturally) to request the change to your visa status. Note that your current visa needs to be for the maximum number of years allowed for that visa type. Until recently this was 3 years for many visas, but with the new immigration system the upper limit for many visas is now 5 years. I'm unclear as to whether you'll now need the 5 instead of the 3 year version, but you are unlikely to get PR if you only have a 1 year visa. See here for the list of requirements on immigration's official site, though it's a little confusing.
- Write a 'letter' translated into Japanese stating the reason you're applying for permanent residence status. There is also a line on the application form asking for this information, but I guess the letter can go into a little more detail. I doubt it has to be very long, it will just need to seem logical to the person evaluating your application. Examples might be planning a family, or wanting to set up your own business in future.
- Have lived in Japan for over 10 years, or be contributing significantly to Japan. Judging from the website however, short of being a Nobel Laureate, being accepted based on your artistic, diplomatic, economic etc. contribution to Japan looks tough. (If you have been married to a Japanese citizen/PR holder for over 3 years, you can apply after just 1 year of living in Japan provided your current visa has the maximum number of years.)
- Show good conduct (have no criminal record).
- Get a certificate of "registered matters" from your ward office showing your current status of residence. (Ask them for a 外国人登録原票記載事項証明書 / gaikokujin touroku genpyo kisai jiko shoumeisho. This is more or less the same information as on your gaijin card, but will also have a record of any changes made and it'll have the ward office's stamp on it. Official documents from the ward office usually cost a few hundred yen to have printed, and they usually make them for you while you wait.)
- Prove stable employment sufficient to support yourself: Get your company to make you a certificate of employment / 在職証明書 / zaishoku shoumeisho and if you have one also submit an up-to-date employment contract / 雇用契約書 / koyou keiyaku sho, along with proof of 3 years of tax payments. For me, proof of tax payments is in the form of withholding tax slips / 源泉徴収票 / gensen choshu hyo from my company and my tax return forms / 確定申告 / kakutei shinkoku, as well as a proof of income tax payment certificate 所得課税証明書 / shotoku kazei shoumeisho from the ward office (also for 3 years) since my current company doesn't process all of my taxes. In your case your company may be able to supply all the necessary information including detail of your ward tax payments as in the next bullet. The lady on the phone at immigration suggested I also include a recent bank statement to show my bank account details and as proof that I'm set up here well enough to support myself. She added that it wasn't a requirement though. As a general rule of thumb from speaking with immigration lawyers, having over 200,000 yen/month wages consistently appears to be a minimum.
- Be paying residence/ward tax (go to your ward office an ask them for a residence tax proof of payment certificate for the last 3 years / 住民税の課税証明書 / jyuminzei no kazei shoumeisho. This might be a recent addition to the requirements which, along with more active chasing up and freezing the bank accounts of non-payers, appears to be part of a bid to get tougher on ward tax evasion/forgetfulness. In my case, the ward office gave me one document that covered all my income and residence tax payments in one go. This all-in-one document was called a 特別区民税・都民税（個人分）証明書 / tokubetsu kuminzei tominzei kojinbun shoumeisho, and they gave me one sheet for each of the last 3 years, showing no tax was outstanding.)
- Be sponsored by a guarantor who is a Japanese national or a holder of permanent residence status. (Have them sign this guarantor document or this one in Japanese. This clause is interesting (read: possibly meaningless), in that on the MOJ website itself it is stated (in Q.7) that the guarantor is not legally bound to the agreement they sign). The guarantor will need to supply proof of their past 12 months' income, their certificate of employment / 在職証明書 / zaishoku shoumeisho, and either their residence certificate / 住民票 / jyumin hyo if they are Japanese, or if they are a permanent resident, their certificate of registered matters (as above for you) / 外国人登録原票記載事項証明書 / gaikokujin touroku genpyo kisai jiko shoumeisho.)
- 8,000 yen stamp for the application fee, which you can get at the convenience store on the ground floor of the immigration building.
- Finally, if an employer or friend can write a letter of recommendation in Japanese, while not required, it is also helpful.
Given that I have been in Japan for over 10 years now and can meet the other requirements, I feel cautiously optimistic about the chances of receiving the status. The application seems to take anything up to 8 months though (update: it took 10 months and was rejected due to length of current stay), while police checks and so on are carried out. I guess the only thing I'm slightly unsure about is whether, after handing in my gaijin card after the JET programme just over 7 years ago, they will count my stay as 10 or 7 years. That, and whether the 'reason' for applying for permanent residency as requested on the application form, needs to be attractive in a particular way.
As reported in a number of places, getting the permanent residence status appears to have no down-side and has the benefit of freeing up the long-term resident vocationally speaking, prevents accidental overstaying on shorter visas and has the additional advantage of rescuing the foreigner living in Japan from annual or triennial trips to the windswept Immigration Bureau on the bay in Shinagawa.
Currently gathering the paperwork for my application. Wish me luck!