It seems like a significant bulk of Japanese novels take place in Tokyo, and with due cause: not only is it the capital, it's home to by far the largest population in Japan. However, there's more to Japan than Tokyo.
With that in mind, GaijinPot has put together a helpful list of 8 Japanese novels set outside of Tokyo, including one of our books, In the Woods of Memory by Shun Medoruma, which they laud as "a study in chaos theory, an exploration of how a single act can have unforeseen and wide-ranging repercussions."
You can read the full GaijinPot compilation here: https://blog.gaijinpot.com/pure-land-8-japanese-novels-set-outside-tokyo/