Out of the veggie restaurants I ate at during my 2 week trip to Japan (September 2012), this was the most traditional Japanese dining experience I had. It's a lovely space with tatami mats and floor seating. It's not all vegetarian, but they were happy to veganize my meal by leaving the fish out. The food was quite good; my friend and I split a meal which had many small dishes (vegan tempura, tofu soup, seaweed/veggies, rice, some bean paste sweets... I'm probably forgetting the rest). They spoke no English though, and without my Japanese-speaking friend I would have had a hard time deciphering the menu and requesting the veggie options.
Cons: Not all vegetarian, No English spoken