Japan can be expensive, but that's only for specific types of restaurants. If you're perusing the 3 star section in Michelin guide and looking for Sukiyabashi Jiro, then Tokyo's going to be pricey. Non-Japanese cuisine like French/American/Italian tend to be a bit pricier for dinner (sorry guys no unlimited apps at TGIFridays for $10).
Fresh produce, specifically fruits, will be very expensive especially when you consider the quantity you're paying for. If you're in the market for a triangle shaped watermelon or a handful of white strawberries pristinely packaged like jewelry, then yes, unfortunately, Japan is going to break the bank.
If you don't fall into any of those above categories and you're totally okay with extremely delicious, satisfying, and unpretentious food, then I'm here to tell you that Tokyo and Japan is perfectly affordable, and for me at least, the greatest place to eat in the world, based on a pure cost : quality : satisfaction ratio (notice how I left out quantity) .