I just made a purchase last week from the Ginza store using the edu discount and they were pretty serious about checking my ID and making copies of my school staff list with my name included (I teach English at a junior high in Japan). If you try to order from the online Apple Japan store, they require you to fax your assigned Japan school student number/teaching credentials to make the edu purchase, then dealing with their English customer service is a whole other headache.
Sorry, but I'm pretty sure you have to be a student/teacher at a Japanese school. Any other opinions?
Dood