There is a wide range of accommodation in Japan, both Western-style and Japanese. Types of accommodation vary widely in terms of style and price. You can choose to stay in the familiar comforts of a Western-style hotel, or enjoy the comfort and personal attention of a traditional Japanese inn or ryokan 旅館.
In addition to hotels and ryokans that can be booked from typical online booking sites such as Expedia, there are less-publicized types of accommodation such as minshuku 民宿, capsule hotels, youth hostels, temple lodgings, camp sites, kyukamura 休暇村 hotels. If you take time to search out, you will be able to find comfortable places to stay that suit your style and budget.