Housing everywhere in Japan is basically free aside from the cost of renovation + the cost of the land. Houses are considered to be disposable there, you're expected to tear it down and build a new one when you buy one, so they are priced accordingly.
The difference is that land in Tokyo etc is expensive.
Old houses in rural areas often need a lot of care due to their age and condition. They may have sat empty for several years and suffered damage from a lack of maintenance.
Also if they're cheap postwar construction, they may not be very earthquake safe. If they're older traditional architecture, they're probably ok but still probably need a lot of TLC.
The difference is that land in Tokyo etc is expensive.