There are many good schools in Japan for ID, but many of them have different areas of expertise/lean.
Tokyo Geidai (University of Arts) has a design department : http://www.geidai.ac.jp/english/art/design.html
Musashino Art University is also prestigious and has produced some designers like Fumie Shibata : Musashino Art University
Chiba University also has a renown design department: Division of Design Science | Graduate School Information | Chiba University Graduate School & Faculty of Engineering
Also check out Tama University: Tama Art University | Academic Programs
Anyways those are off the top of my head universities that are pretty big into design.