I’m always a sucker for Tokyo Hands, but in the Japan Craft Journal, I found links to a lot of other stores. Some I’ve heard of (Tomato, Okadaya [have I been here?], some I’ve not.
Okadaya – Giant six-storey fabric crafts store near Shinjuku
Tomato – fabric store in Textile Town.
Fabric shopping at Marunan in Shibuya and Yuzawaya in Kichijoji plus small guidance on flea markets.
Tokyo Shopping Guide (emphasis seems to be on shopping, not actual raw materials)
I’ve never heard of the Ito-Ya stationary center in Ginza
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