Just watched David Cheng's Mind of a Chef over the weekend so this is fresh in my mind - a few of his episodes are based on Japan.
It seemed like almost all of the food contained some sort of fish product, from obvious things such as fish/sushi to less obvious things such as soups and marinades which have fish sauce, shrimp paste, etc.
So just be on the lookout - "no seafood" be a useful phrase to learn to check with the waiter before eating.
Best of luck and safe travels!