Many universities in Japan offer German language courses as well as programs in German Area Studies. For further information please consult the individual websites.
Other alternatives are Japanese-German Associations, which also provide language courses.
The Goethe-Institut offers worldwide language courses at all levels. In Japan courses are available at the locations in Tokyo, Yokohama, Kyoto and Osaka. Furthermore you can take correspondence courses via internet.
“Schools: Partners for the Future” (PASCH)
The project “Schools: Partners for the Future” (PASCH) supports and unite, coordinated by the Federal Foreign Office, more than 1800 PASCH schools in a global network. Part of the initiative is sustaining young people’s interest in and enthusiasm for contemporary Germany and the German language. In Japan there are various German schools as well as schools, at which German language courses and area studies had been expanded.