Kyoto Municipal Museum of School History
http://kyo-gakurehaku.jp/Default.htm has a collection of Edo period through WWII era materials on schooling in the city of Kyoto.
Tottori Prefectural Archives
Several years ago archivists there made copies of the historical documents held by every public school in the prefecture and catalogued the copies in the prefectural archives.
Kaichi gakkou (Kaichi primary school)
Several tens of thousands of documents have been preserved and archived from the Kaichi gakkou primary school which dates from 1873 in the city of Matsumoto, Nagano Prefecture. Twenty or so volumes of this material have been reproduced and published.
Shinano kyouiku hakubutsukan (Shinano museum of education)
This small facility in Nagano City, Nagano Prefecture has a collection of textbooks dating from the end of the Edo period, historical journals of the Shinano kyouikukai (a local teachers' association), children's artwork, etc.
The library (http://www.nier.go.jp/library/) of the National Institute for Educational Policy Research in Tokyo has government documents, textbooks, and other materials on education primarily from the late 19th century to the present.
Materials can also be found in many major university libraries, the National Diet Library, and other government archives, municipal museums, as well as in schools themselves. The oldest public school in a particular area sometimes has administrative logs and other materials dating to the institution's founding sitting in a safe in the principal's office. Public schools in Japan are frequently being combined in recent years as the number of school age children declines, so if one can find a school that traces its ancestry to several older ones, and obtain permission from the principal to have a look, a treasure of historical materials may be waiting.