This database lists 363 language schools throughout Japan, many of which are located in the major cities with about 40% found in Tokyo alone. Most schools are private language institutions, but some are attached to universities, colleges, and technical training schools—or are affiliated with a governmental organization.
You can use the database to search for Japanese language schools in Tokyo (and areas within Tokyo, e.g. Shinjuku, Shibuya, etc.) or other locations, as well as by course type/study purpose and by nationalities of other students. See here for general advice on how to choose the best Japanese language schools.