We Make Money Not Art has a great roundup of Japanese universities that are creating centers and programs for the study of manga:
According to asahi.com, Kyoto Seika University created the first school of Cartoon & Comic Art in Japan in 2000. That was the beginning. This spring, additional three universities created similar schools and courses for students to study manga, anime and games.
Osaka University of Art recently created Character Creative Arts Department. The dean of the department is comic artist Kazuo Koike and at least two of the 23 professors are well-known comic artists (Go Nagai who created Mazinger Z, Devil Man, Harenchi Gakuen, etc. and Machiko Satonaka who created Ariesu no Otome, Asunaro Zaka, etc.).
This April, Takara Zoukei University created School of Media Contents with a focus on movies, animation, and games. Professor Reiji Matsumoto is a well-known comic artist who created Space Battleship Yamato, Galaxy Express 999, etc. He recently did some anime work for French band Daftpunk.
Finally Otemae University recently created a manga and animation course. Monkey Punch is a professor there.