Perhaps the most attractive cycling road in Japan is 70 kilometers’ “Shimanami Kaido” from Onomichi (Hiroshima Pref, Honshu Main Island) to Imabari (Ehime Pref, Shikoku Island).
It crosses Seto Naikai Inland Sea and you will enjoy beautiful scenery and nice foods along the way. Interestingly, long bridges over the sea have automobile highway lanes as well as bicycle and pedestrian lanes separately.
This is very popular cycling route to many Japanese as well as international tourists.
I have been there twice, once by my own bike and once by using rental bike.