Japan is a very beautiful country with lots to experience.
Its like experienceing something new each day. It will not stop to awe you. But being a vegetarian poses some problems. They are farily unknown to the concept of vegetarianism. So prepare yourself ahead to enjoy Japan without going hungry! :-)
Best thing to do is, equip yourself with some instant food from your home country (we found cup noodles to be our saviour in Japan). Also you can cook a bit, if you stay in a hostel as they have a kitchen attached, plan your stays accordingly (I used to carry my lunch pack with me, if I am travelling to an interior place).
Apart from that you can buy very good fruits, juices, dairy products (milk and curd; again cheese might be a problem as they may be made from animal renette) and bakery items (our personal favorites being the cream buns). And if you really want to try something out, you can try the cold soba noodles (hot ones come in a broth, which might be from fish or chicken), or the rice balls with sea-weed sheets; but they are highly tasteless.
Buying anything from stores also needs some care. Most of the products don't come with anything written in English and you might not even find a English speaking staff in many stores.
So prepare yourself with phrases like -
No meat - "MiitoNae"
No fish - "Sakana Nae"
No egg - "Tamago Nae"
No ham - "Hamu Nae"
No beef - "Biifu Nae"
No chicken - "Chikin Nae"
No pork - "P?ku Nae"
No gelatin - "Zerachin Nae"
No lecithin - "Reshicin Nae"
No fish stock - "Dashi Nae"
No Bonito Flakes - "Katsuo-bushi Nae"
Use these phrases in a questioning tone with appropriate gestures, that will drive your point!
Next, you can find some vegetarian restaurants in Japan. Do a bit of research over the Internet. Most of the Buddhist and Indian restaurants, you can find some vegetarian dishes. But sometimes, there is nothing near to your place, so always be prepared to fall back on other things.
If you don't eat egg as well, be sure to confirm that in the restaurants, as most of the veggie restaurants are actually ovo-lacto vegetarian. I have had the experience of the Indian Breads having egg, so had to always do with only rice and curry.
Chocolates - you can find some european chocolates in some of the stores, majorly "Lindt". And for something local, most of the "Meiji" chocolates are safe.
So prepare well in advance and you will have a wonderful time in Japan. As to popular thought that you cannot survive much as a vegetarian, its not true. I survived for two months, so can anybody!! :-)