Well, correct me if I'm wrong, but as far as I know Japan does not offer the same range of gluten free and paleo type products western countries do. I've read about celiacs living in Japan and it is quite difficult.
Organic food is not really what I need anyway. I need access to health foods like quiona, buckwheat, stevia products and paleo alternatives for a balanced diet. Organic restaurants would be ideal, but as far as I've there are not that many and it is quite pricey.
It wouldn't surprise me if Japan doesn't have strong health culture. Their diets might seem healthy to an average westerner, but in reality Japanese cuisine tends to emphasise sugary white rice, which is not healthy at all, as well a low-protein diet, excessive use of high sodium soy sauce, improper food combining and lots of sugary snacks/drinks. That doesn't seem healthy to me at all.