¥900,000 is almost exactly what I spent on average over a 5 year period from 2007-2012 living in rural Japan (Shizuoka prefecture). A couple of caveats: I was single at the time. I had subsidized housing (worth about ¥250,000 yen a year). I didn't have a car. That was the money I spent, and I made considerably more than that so was able to save quite a lot. However, I was very comfortable with that level of expenditure and I can't think of anything basic that I lacked.

I think you would have to budget fairly tightly and it would be pretty easy to get into trouble. Especially in the north where you have to pay for heating it might be dicey. But it's not impossible to live relatively comfortably. I ate out a lot and drank expensive beer a lot. If I cooked more at home, ate more fish and drank shochu I could have saved more money. Getting rid of the TV (and thus the monthly NHK bill) would be fairly substantial.

I have a lot of single friends in the area who make ~¥2,000,000 a year and they are absolutely fine on that salary. It's a different lifestyle from what people in the west are used to, but I wouldn't say they are less happy.