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Shibuya, Tokyo: Unlike many vegetarian restaurants in Japan that tend to have only a few plate-lunch style specials, Nagi's menu is varied, with over a dozen dishes to pick and choose from, not to mention a healthy list of libations. Some choicey bits are the soy meat with sweet chili sauce, reminiscent of karaage (Japanese fried chicken), a tofu and veggie curry simmered in coconut milk, a kabocha squash salad, a stir fry with mushrooms, peppers, broccoli, and carrots, and many other colorful and mouthwatering dishes.
Vegetarian ramen seller in a busy restaurant in Tokyo station
Alishan Organic Center and Cafe has a great variety of organic, vegetarian and vegan friendly food all served up in an enchanting, riverside setting only an hour from Tokyo. 
Enjoy delicious Chinese, Japanese and vegetarian food at lovely Heianraku, a cozy restaurant in Takayama.
Interesting Juice Bar hidden behind Kaminari-mon, Asakusa
Potasta is a Tokyo must-eat: healthy sandwiches overflowing with organic vegetables