Cheap housing in Tokyo?

After having spent a few weeks on the road I have now settled down in Tokyo and will stay here until the end of my stay in Japan. Which is not that far away by the way, which feels strange. But I am coming back, so that's ok.
My arrival in Tokyo should have been smooth, I had booked a guesthouse in advance and thought the accomodation would be settled. The place had looked nice enough on the internet and was both cheap and central. When I went to pick up the keys I paid half of the one month rent already. But the place turned out to be - eeehm, well, it's hard to call it anything else than a rathole! Imagine an old shabby building next to a noisy railway line. Two walls of your "room" are not real walls but 1) a thin-"hear whatever your neighbour does" panel separating it from the next room. While a second wall consists of a row of metall lockers where people put stuff in and take some out all day and night. And yes, metall lockers DO make noise when being opened. Other features of the proposed accomodation would be a tiny dirty kitchen and and equally tiny and dirty bathroom, squeaking doors, lacking isolation and a leaking roof that requires pots to be placed everywhere to collect valuable natural rain water... And I am NOT exaggerating, this place was a dump.
I tried to convince myself that it was not that bad, but I felt really uncomfortable there.
So I went to tell the agency the next morning and told them I intended to stay just one more night and wanted my money back. Well, they could have made troubles about the money, because the contractual notice period is 2 weeks (and I had paid for 2 weeks..). Maybe it was my luck that they were Japanese, instead of making trouble they apologized a thousand times and gave me back the money without any discussion. The harmony seeking nature of Japanese culture can be an advantage sometimes...
And I learned that you really can't have a cheap (380 CHF a month), central AND nice apartment. You need to make some concessions. And I decided that next time it would not be the "nice" part...