[Barone1551]

Some simple things:
-Food has less fat, but is pretty salty. But no more salty than in the US
-Portions are far smaller
-Food tend to be less processed than they are in the US (but not always)
-People tend to drive less, they usually walk, ride bikes, or take public transportation which involves walking there.

These are some of the reasons. The sad truth is that there are people all over the world who have eating disorders due to a degree of things. However this is not the reason Japan as a country is skinny. They are skinny becuase of a diet that has low protein and lots of grains, rice, and fish.

EDIT: and to comment on the above posts, It is true many people I have know that have moved to Japan even for a short time lost weight. And vice versa, almost all of the exchange students we get from Japan gain weight while they are in the US.