There are several types of accommodation in Japan as same as in Europe but the unique one is accommodation called Ryokan. Ryokan is the traditional Japanese inn, which usually offer stay including half board and equipped with large bath inside the building which all guests can be used.
Then, ryokan offers basically two types of guest rooms. The first one is called Yoshitsu which means western room, which is as same as in Europe, room equipped with bed or beds. Floors of these rooms are usually carpets and you do not have to take off your shoes. The other one is called Washitsu. The floor is not carpet but tatami, and you have to take off your shoes before stepping on the tatami floor. Then, Washitsu does not have bed and therefore you have to sleep on the futon.
Ryokan used to offer only Washitsu type rooms till 90s but due to many Japanese now prefer to sleep on beds, especially elder people, ryokan with yoshitsu are increasing. Many ryokan also offer room called Yowashitsu, which is hybrid type; combination of tatami and beds. There are two rooms, one room with beds on a carpet and the other one with tatami. Yowashitsu can be considerd as Japanese version of suite room too.