I already asked a similar question (but regarding Samue). I tried to search around, but didn't manage to get any confirmation that they can be bought in same areas.
You're looking for a pretty obscure bit of kit, most Zen temples I've been to in Japan frown on frippery like comfortable cushions for meditation. But you should be able to find these in a well-stocked Buddhist goods store, and here are a couple with an online presence that claim to have them in stock:
- Butsudanya Takita Shoten (仏壇屋 滝田商店), Kotobuki 2-8-11, Taito, Tokyo, near the famed Sensoji Temple in Asakusa. This bad boy is Y4510, and they've got others as well.
- Negishi Futon (根岸ふとん店), this is actually a small chain but one outlet is in Nozawa 2-5-23, Setagaya, Tokyo. Y9800 for this set of two, which is apparently the Official Meditation Cushion(tm) of the Rinzai Zen sect and is used by the Tokyo Zen Center.
Alternatively, if you're actually planning to study meditation in Japan, I'm sure the temples can either hook you up or sell you one directly.
I can't really tell if this is a physical storefront or solely an online presence, even after looking at Street View, though it should be easy enough to contact them and find out. In the latter case, it shouldn't be difficult to arrange for delivery.
Butsudanya Takita Shoten is under construction at the moment. Near Tawaramachi station there is a line of Budsudanya shops, I found the zazen zabuton in one of them, but there is need to ask, I didn't see any at the shop window. Here is the streetview image of the shops.