So... you've received your Japanese pension refund after 6-36 months service in Nippon. A few hundred thousand yen in your trusty bank account. Now, what to do to receive the tax refund? After all, it's 20% of your total pension refund.
Well, for one, you should have designated a tax representative to act on your behalf before you left Japan. If you didn't do this, it's too late for you. Sorry. Tax representatives can be appointed with a "Declaration Naming a Person to Administer the Taxpayer’s Tax Affairs (for use by aliens)" form at your local tax office. If you need the kanji for the paperwork, it's 納税管理人の届出書（外国人用）.
1. In Japan, file your 納税管理人の届出書 form at a tax office.
2. Outside Japan, send in your pension refund paperwork.
3. Receive the pension refund receipt. Mail the original receipt to your tax representative in Japan. He or she will then go to the tax office and file the final paperwork (確定申告書) on your behalf.
4. Your tax refund will be deposited into your tax representative's Japanese bank account.
5. Your tax representative can mail you an international money order or wire the refund.