Here some notes on those web pages I have found most helpful for tour planning. See also this blog post about cycling roads.
- Proposed cycling courses, ordered by things such as "mountain", "along rivers"... Possibility to select based on map. Except Saitama (and maybe a few other places) the bicycle roads are the same as from the MLIT (see below)
- Cycling the length of Japan, but often through the mountains, with elevation maps, but not very detailed tour descriptions
- Cycling paths from the ministry. Quite badly made web page, which also does not seem to be maintained since many many years, but it is still the only place I could find the 135 official bicycle lanes in Japan.
- http://www.mlit.go.jp/road/road/bicycle/road/index.html (does not work anymore)
- Kancycling, this web page has good ideas for tours, but no detailed maps.
- Panasonic, list of proposed cycle courses in Japan, that can be selected from a map. Also if you register maps can be downloaded.
- 11 different routes through Hokkaido: http://www.14degrees.org/hokkaido-cycle-touring-routes/
- Cycling in and around Kyoto: http://www.cyclekyoto.com/
- List of bikeshops etc: http://www.cycling-tomorrow.jp/ 日本語