Japan offers a variety of accommodations ranging from Western-style hotels to traditional Japanese inns called ryokans. Travelers with a spiritual interest, however, should take advantage of the network of temples that offer guest rooms.
Prices are reasonable, typically between $50 and $100 a night (which often includes breakfast and/or dinner). Accommodations vary depending upon the size of the temple, but you can often reserve a private room, though baths and restrooms are typically communal. You will likely sleep on a futon in a room with sliding paper screens. Some temples allow guests to observe rituals and you will also have access to the grounds of the temple complex when it is closed to the rest of the public (a great advantage).
Temple Lodging in Japan gives useful information on temples across the country that take visitors.