The entire refund process takes up to a year to complete and is in two parts. You apply directly to the Japan Pension Service in Tokyo for a lump sum withdrawal (pension refund). The Japan Pension Service send the refund to your bank in your home country, but hold back 20% as income tax. You then have someone in Japan (we will do it at Shidoka, if you'd like) act as your agent to apply for the 20% tax, and s/he sends it to you.
You must file for the pension refund within two years of withdrawing from the scheme (whether you stay in Japan or not), and for the tax refund within five years of withdrawing from the scheme.
The amount of refund you receive depends on how long you've been here. As long as you were properly registered, you will receive roughly the equivalent of one month's pay for every year you've been in Japan (up to a maximum of three years).
There are several stages to the application procedure.