I love tokyo, but tbh, I don't think it's particularly clean? At least when I went there was a fair bit of rubbish around the place; certainly not as much as you'd find in most of Europe but definitely far far more than you'd expect given the cities reputation. I find most of Australia ~as clean.
Strange, I walked in different regions of Tokyo, and I found it to be very clean. This is in part because in Japan it is not done to eat while walking in the street.
I remember that in Osaka on Saturday night there were young people kicking trash around, that was the only time I found Japan dirty.
Were you staying in Shinjuku or Shibuya? Those areas can get particularly dirty in recent years. I think overall Tokyo is still pretty clean in comparison from other places I've lived or traveled though.
