The desirable cities with lots of jobs. OTOH, some rural towns are so desperate for people they'll give you a house for free (or nearly free).

https://www.rethinktokyo.com/free-houses-japan-countryside

Just select cities. I had a decent bachelor pad from 2014 to 2020 that was 55,000 yen (~$550 at the time) with no rent adjustment over that time either, and I'm in an urban area of ~1 million people. Current place is ~82,000 but with the Yen getting body-slammed by the US dollar it's not that much more expensive.