This is one of the struggles of being vegan, I guess. Japan is a lovely country, known for its culture. Their food is also mouthwatering. I remember going there a few years back (wasn't vegan yet) and I know for a fact that it's hard to know which is vegan, which is not. And honestly, it's hard to resist. Even their ramen broth, being one of the best things about their country, is made of meat so it does suck.
But yeah, the tips posted above would help you. Happy travelling!