First Registraion Tasks for your NPO

You may feel relieved when you received the certification letter of establishment from the local prefectural government.
Unfortunately, it is too early.
Your NPO is not officially established unless you register it with your local Legal Affairs Bureau. 

You may wonder what is the Legal Affairs Bureau. 
They are a governmental organization and a part of the Ministry of Justice. They cover a wide range of services but the most famous ones should be company and real estate registration.
The Ministry of Justice provides an English website explaining who they are, but it may be more confusing than my explanation.
https://www.moj.go.jp/ENGLISH/m_hisho06_00034.html

As I described before, I spend almost 30 years as a local government officer and have been wondering throughout my career why many government websites seem to be never proofread. 

Let's get back on track.
They have their head office in Tokyo, 8 main branches, and 42 branches across Japan.
Each branch has smaller local offices which have limited capability. For example, some local offices can only issue registration certifications and do not take registration applications.
Please check their website to find the branch which administrates your NPO's head office area and offers corporate registration service. 
Kankatsu no Goannai (Japanese)
https://houmukyoku.moj.go.jp/homu/static/kankatsu_index.html

To register your NPO, you have to file those documents as follows,
1 The application for registration
※Sample Form with instructions (Japanese)
　https://houmukyoku.moj.go.jp/homu/content/001252905.pdf
2 The article of incorporation
3 The letter of certification of establishment from your local government
4 CD-R or DVD-R with all information in the application for registration

In the application, you have to contain the name of your NPO, main office address, and reason for registration (Please write the receiving date of the certification of the establishment. You received it, so you want to register. That is the reason for registration. Really.), the receiving date of the certification of the establishment. Please refer sample form above.

They require to file original documents including the article of incorporation and the certification of establishment, but never give them to them because those documents are so essential.
You have to take a copy of those documents and write "This is the copy of original documents", your name and the date on the last page.
Then press your official seal (Hanko) on each page.
Unfortunately, all has to be done in Japanese. 

Although you can file your application by mail or online, I strongly recommend going there for yourself.
If there is just one slight mistake in your documents, they will send all documents back to you if you do it by mail.
If you want to do it online, you have to obtain the electrical certification in advance and download their software and.... I recommend doing so if you establish NPOs quite often like three times a year.
Moreover, officials in the Legal Affairs Bureau are usually kind enough to give you advice and are happy to check your application on-site. So you should go.

At the same time, you should register your NPO's official seal (Hanko) to the Legal Affairs Bureau. Then you do not have to go there twice.
The application is one paper and rather simple. Please do not forget to bring the seal with you. 
https://houmukyoku.moj.go.jp/homu/content/001188611.pdf

You can download all forms including sample form with instructions here. All in Japanese. Cross fingers.
https://houmukyoku.moj.go.jp/homu/COMMERCE_11-1.html#4-1