One of the largest organic, low chemical and natural food stores in Japan has just launched its English site. The prices are higher than your local supermarket but if you are used to shopping at the big international supermarkets in Minato-ku then you might think it is cheap! The English descriptions are not available yet but some of the products do show the area that they were grown. Don't expect foreign brands, it is very Japanese.
If you make your own baby cereal they have organic millet, barley and brown rice in the Rice/Bread/Noodles section. There is also a small selection of organic baby food.
Radish Boya eshop