I believe that there are a lot of vegetarians in Japan. There is a rather popular magazine called, "Ready, Veggie, Go!" You know that Bhuddism has a long history of vegetarianism as well as Janism, though it is not directly related to the question of Japan. I know that I have also eaten at vegetarian restaraunts in Japan. Watch out for any soup broths, dumplings etc. I will also let you know that there are plenty of wonderful vegetable shops in Japan and lots of great fruit. Yummy!
Here is a listing of vegetarian tokyo restaraunts:
Tokyo Vegetarian Guide: Vegetarian-friendly Restaurant Guide