While I certainly saw lots of fabric and crafts, I was surprised that I didn't see much specifically for quilters in the places I visited. For example, we visited a few magazine stores and although there were handicraft magazines for knitters, crocheters, and general crafters, I only found one quilting magazine which was Quilts Japan. We spent a fair amount of time in three bookstores in Tokyo and one second bookstore (BookOff), as well as in the book sections of various fabric and craft stores, and the quilting sections were microscopic compared to the large dressmaking sections or even the knitting/crocheting sections. Tatting and jewellery making were also well represented. And most of the quilting books they had were about making bags and accessories, only a couple were for bed quilts. It made me wonder if quilting isn't as popular right now?
Googling on anything related to fabric in Japan will probably lead you to Nippori Fabric Town, a neighbourhood in Tokyo where there are a lot of fabric stores including the famous Tomato. I also hit a couple of branches of Tokyu Hands (a lifestyle and craft store chain), the Okadaya fabric store in Shinjuku, and the two branches of the excellent Nomura Tailor fabric stores in Kyoto. Some of the shops stocked a lot of imported American quilting cottons, as well as Japanese versions including Japanese copies of Liberty prints. Most of the Nippori shops did not sell much in the way of small cuts, they wanted you to buy a half or whole metre. Because of our dire exchange rate at the moment, prices were similar to the UK but I met some American quilters who were exclaiming that the prices for quilting cotton were lower than in the States. Some shops were displaying made-up samples of bags or clothing, but not any quilts.
I focused on Japanese fabrics as I wanted a souvenir of my trip, but I didn't want to load my suitcases with a lot of yardage so I was fairly restrained.
So fabric is readily available in Japan and there must be a lot of people sewing clothes and household items judging by the books and patterns I saw. There were some big haberdashery sections in most of these stores as well, I was tempted by the large selection of bag handles at good prices but as I didn't have a specific project in mind, I didn't get any in the end. If you do go, I suggest taking a few project ideas with you as it can be a bit overwhelming in Nippori where there is so much choice.
There are many good blog posts online about where to find fabric and craft shops in Tokyo, Kyoto etc so do your research before you go. It can be difficult to find places once you're there as addresses don't really work well in Japan (many streets aren't labelled and they don't number buildings consecutively) so search particularly for written directions on how to find places like Okadaya, and even better for photographs of the shop fronts since you may not be able to read the shop signs. I took a handful of printed notes with me including photos, directions, screenprints of Google Maps etc which really helped. Don't worry if you don't speak Japanese because the shop clerks will always type out the total price on a calculator if there isn't a till display and show it to you and most of the price tickets have at least the number written out in roman numerals. Fabric is sold in meters so either learn the numbers up to ten in Japanese or hold up the appropriate number of fingers, or if all else fails use your hands to indicate on the metre stick how much you want. Very likely the clerk will speak some English as it is taught in schools. Most shops will only take cash, credit cards are not widely used in Japan, but everybody seems to have lots of change so it's easy to break bigger notes like a 10,000 yen note. Happy Fabric Hunting!