It would be an understatement to say that the supermarkets in Japan are different than those in America. Since the land upon which food grows, is harvested, is planted, the type of soil on an island versus a larger continent less Hawaii etc. there is so many things that are different that it would be better to compare the similarities.
Instead I wanted to share a few things of note about the cost and types of food that I have come across personally. There is a huge difference in the quality of goods in a Japanese supermarket, and an American supermarket. In Japan, on the whole, the quality of fruits and vegetables is more than excellent. The Japanese are very picky about what they eat, and the quality of service is so competitive, it makes for good groceries. Unless the fruit or vegetables are 100% blemish free then to the Japanese the produce is deemed unrepresentable.
Sake talkie will be taking a look at the Japanese GOBO, or burdock root, in future editions. For now, I want to discuss 牛乳 or gyu^nyu^ milk. Milk in Japan does not come in gallons and they don't often buy as much at a time as Americans (2 gallons for $6-7 bucks). And Japanese milk tastes terrible. There were two things I wanted when I came back from a trip to Japan; the first thing was a good old glass of USDA pasteurized whole fat milk. Because the way Japanese milk is pasteurized is different is why I suspect it tastes so bad. I read on the label that they pasteurize it at a much high temperature in less time than Americans. Like 128º for 15 sec. vs the American pasteurization technique which typically is 68ºC (145ºF) for 30 minutes. The other thing being peanut butter, because the Japanese have none!