It is hard to generalize entire Japan as one hole thing, obviously it will be more expensive at a place like Tokyo and Osaka. If you spend time at country side then a cost will be lower. I agree with ksandness, I always tell people that if you keep the standard of your home country then it will cost more in Japan. If you go about like locals do in Tokyo then Tokyo can be a lot cheaper place than you think. That means if you insist of staying at a place like Hilton and Sheraton then a cost of lodging will be higher. Typical Japanese businessmen on a business trip to Tokyo do not stay at a hotel like Hilton, Hyatt, Sheraton, etc. Non-management Japanese business travelers on a business trip to Tokyo usually stay at business hotels, which has a room a lot smaller, beds smaller, and bathroom a lot smaller than Hilton, Sheraton, or Hyatt. But has to understand that is the standard in Japan. Cannot keep the standard of your back home and expect thing to be cheap in Japan.

Even here at FlyerTalk many ask about Michelin starred restaurants and best sushi restaurants in Tokyo, but average middle class Japanese in Tokyo do not eat at places like that. Even at a fancy shopping district at Ginza, all I have to do is step a block or two away from main street and walk along smaller side street and easily find mom and pop hole in the wall kind of a place. Here at FlyerTalk pretty much everybody talk about staying and having meals at the central area of Tokyo. Simply going out to suburb of Tokyo and can easily find stores and restaurants locals frequent, but those will be very different from "sushi and tempura" place you seen back home.

I tell visitors that do as locals do at Tokyo and cost can be surprisingly lower, but likely the lodging can be outside of your comfort zone and food will be nothing like what you have imagined from back home.