ALTs on the JET Programme must receive a United States Residency Certificate (form 6166) in order to be exempt from Japanese taxes. This certificate must show that you were a US resident during the year prior to coming to Japan through the JET Programme.
To obtain this certificate, download the application form 8802(pdf). Fill out as necessary (if you have questions, first check the instructions for form 8802 here - pdf), and send it to the appropriate IRS location by mail or fax (see instructions). The IRS will charge a $US 35 fee for any applications postmarked after November 1st, so in order to avoid that fee send in your application ASAP if you have not done so already. After sending in the application, your Certificate (form 6166) should be sent back to you, and this should be filed with your Japanese tax exemption form. *This does not apply to CIRs, SEAs, or 3rd year ALTs *This only affects Japanese taxes. US taxes must also be filed by the appropriate time. *This certificate is good for two years, so if you already submitted it last year there is no need to submit it again this year. For a few more details, see the JET Programme homepage, check your General Handbook, or contact the JET Line at 03-3591-5487.