There are several ways to purchase a futon in Japan.
You can purchase the item at futon shops which are generally located on shopping streets and offer a wide variety of goods such as a standard futon, the luxurious ones for weddings, the small ones for children, and other various futon-related goods. Some futon shops also offer a futon cleaning service or a futon re-fabrication service called uchi-naoshi. And the futon professionals work there, you can consult them. More and more futon shops are opening the online shops and offering their unique products.
You can also purchase the futon at furniture shops which usually sell the bedding set. In some large-scaled furniture shops, you are allowed to try several products such as a pillow and a futon to see how the product would be comfortable for yourself. They have a wide selection of products, so it may be suitable for those who want to actually see, touch and use the item before buying it.
You can also purchase the item online. Most of online shops are usually operated by the futon shops and high-grade goods or original goods are available there.
If you want to buy the futon at a reasonable price, it would be good to buy online, because the online shops usually offer mass-produced futons at lower price than actual shops. If you buy online, a futon cleaning or uchi-naoshi service may not be available later in some cases.
Therefore if you use the futon for a long time, it would be good to buy the high-grade one even if it is a little expensive.