7-11 lawson and the like will charge you quite a bit.
Easily $1.50 for one banana, $1+ for an apple, etc.
Avoid Tokyo Station stores as well - they're selling up to $30 apples and other fruits, mostly as gifts.
supermarkets are decent, but generally expect most fruits to go for 2x+ the normal price until you've found a resonable supermarket. Also, some fruits are never really cheap - melons - because they're mostly used as gifts. In general, the lack of significant imports means the fruit prices are expensive since many are home-grown and raised.
Pretty much most things green and fruity will cost you until you find a decent supermarket, and then, you'll be suprised now and then. Definitely nowhere as cheap as the crazy low-priced Chinese/Asian supermarkets here in Los Angeles! (then again, some of these supermarkets in LA have been shut down due to food violations.....)
The lack of lots of vegis/fruits + high sodium Japanese foods is one reason they've got a high colon cancer rate, too.....
Now, as for crazy prices, talking about rice ....