Wow, that huge for Japan I believe.
I live at Kichijoji and it takes me 1 hour to get to work in Akasaka. I love my place and somehow get used to this routine, but honestly I wish I could rent a place in Japanese countryside.
Building a new house in Japan is surprisingly affordable, but getting one built to Western standards (say, effective insulation and an expected lifespan of more than 20 years) is not. And I'm not even being facetious here: Japanese building codes assume that wooden houses last for 20 and concrete ones for thirty, then they get torn down and rebuilt by the next land owner.
Focusing on the abandoned houses is a bit of a red herring, though. There is definitely affordable non-free housing to be found in Japan... less than $100K USD for a move-in ready house in a small city seems very doable to me.