Get a passport application from your local passport office. In Tokyo, contact the passport section of the metropolitan government (ten-cho). Applicants outside Tokyo should apply at their prefecture's government (ken-cho). You will need two copies of this application form. Since 2006, all passports have contained a biometric identity chip.
Take a passport photo. Photos must conform to EU standards. They must measure 45 by 35 mm with the height of the face from 32 mm to 36 mm. The picture must be taken full face (no hats or other head adornment) against a white background. Passport photos can be taken by a photographer or composed online but must meet all specifications and be signed on the reverse side. One copy is required if applying inside Japan and two are required if applying outside the country.
Collect official copies of your identification documents. You'll need certified copies of your family register (koseki shohon/tohon) and certificate of residence (jumin hyo). Both must be dated within six months of the day you apply for your passport.
Take your driver's license (unten menkyo sho) or health insurance certificate (kenko hoken sho) for personal identification. Employee or student identification cards with photos may also be used as identification. You should also take your personal stamp (hanko).
Take your completed application and these identification materials to the passport office. You should also bring any expired passport and a self-addressed (to the same address as is listed on your certificate of residence) post card with you. You will be given a receipt for your materials.
Your the postcard should arrive in about a week, advising you that your passport is ready. Take it with your document receipt and your passport fee to the passport office to pick up your new document. Be sure to check that the personal information is correct.