Hi sizuku,
I know how hard it must be for you to be celiac in Japan. I have spent 1.5 years in Japan and it was a challenge for me. 100% of people I met have never heard of this problem, and eating out was a real problem since all Japanese brands of soy sauce have wheat flour listed in ingredients... Also, as far as I researched on the Internet, there are no gluten-free bakeries within Japan, you would have to individually import products from abroad to have bread
However, I found one company that makes 100% rice bread that is really tasty

They are in Hokkaido, but I know you can buy their bread in one shop in Tokyo, so maybe they sell in other places in Japan also. I don't know where do you live in Japan, but if you need an adress I can give you -or you can try browsing the web for BRICE (that is the name of the bread), as I'm afraid this site will not display Japanese characters correctly if I post them

Ganbatte ne!
Anna