Jul 17, 2018
Specifically for US Citizens, as that's what I know, but possibly similar for others.
First go to this link to check for your closest US Embassy (Akasaka Tokyo) or Consulate. (Mouseover on Embassy & Consulates on the top right then select for details.)
There are only five consulates in Japan, but they're centered around the biggest cities and spread among regions. They're located in Sapporo, Nagoya, Osaka/Kobe, Fukuoka, and Naha.
Keep in mind that these offices will be closed on both Japanese and US national holidays.
Appointments (booked online) are required for passport services and are not always easy to make. There are limited spots available, especially at Consulates.
The nice thing about US passport renewal is that it can also be done by mail if it's too far or too much trouble to make an appointment at a consulate. By mail can be faster than going into an office unless you're in the same city, but you'll need additional paperwork and a trip to the post office. The processing time is 3-4 weeks either way.
The link for passport services. You'll want to click on renewals if that's what you need, but there's also a link to replace lost or stolen passports.
From the renewals page, you'll need to click on 'by mail' or 'in person.' There will be a checklist of everything you will need. You can find the details or links to them on the passport services pages.
The quick list:
Your current passport
Proof of ID (US Drivers License for example)
A passport photo (check for specifications)
A self addressed JP Letterpack for delivery of your new passport
The passport fee
Payments can be made in US cash in an office, but check if credit cards or yen are accepted at your closest office and have a back up option. If your name on the passport doesn't match your current ID, you'll need proof of a name change too.
If renewing by mail, you'll need to fill out a form as well (link to the form on the webpage). You'll need to pay by International money order and there are instructions on the site for how to get one from your post office. Note that the address to put on the money order is different from where you will send the renewal documents to. You'll send the package off to your closest Embassy or Consulate in Japan. Use insured and tracked mail and don't forget to peel off the tracking number before sending the package, like I did.