In addition to the usual youth hostels and business hotels, you can find several kinds of uniquely Japanese accommodation, ranging from rarefied ryokan inns to strictly functional capsule hotels and utterly over-the-top love hotels.
When reserving any Japanese accommodations, bear in mind that many smaller operations may hesitate to accept foreigners, fearing language difficulties or other cultural misunderstandings. This is to some extent institutionalized: large travel agency databases note the few hotels are prepared to handle foreigners, and they may tell you that all lodgings are booked if only these are full.Instead of calling up in English, you may find it better to get a Japanese acquaintance or local tourist office to make the booking for you. Alternatively, for cheap Internet rates, Rakuten's English search tool (http://travel.rakuten.co....) is a valuable utility. Note that prices are almost always given per person not per room. Otherwise, you may have a rather unpleasant shock when your party of five tries to check out..
When checking in to any type of accommodation, the hotel is, by law, required to make a copy of your passport unless you are a resident of Japan. It is a good idea, especially if you are travelling in groups, to present the clerk a photo copy of your passport to speed up check-in. Aside from this, remember that Japan is mostly a cash only country, and credit cards are usually not accepted in smaller forms of accommodation, including, but not limited to, small business hotels. Bring enough cash to be able to pay in advance.
One thing to beware in wintertime: traditional Japanese houses are designed to be cool in summer, which all too often means that they are freezing cold inside in winter. Bulk up on clothing and make good use of the bathing facilities to stay warm; fortunately, futon bedding is usually quite warm and getting a good night's sleep is rarely a problem.
While accommodation in Japan is expensive, you may find that you can comfortably use a lower standard of hotel than you would in other countries. Shared baths will usually be spotless, and theft is very unusual in Japan. Just don't expect to sleep in late: check-out time is invariably 10 AM, and any extensions to this will have to be paid for.
You may have difficulty finding rooms at the busiest holiday times, such as "Golden Week" at the beginning of May; and prices are commonly higher on Saturday nights. But Toyoko-inn business hotels in towns not listed in your guidebook often have vacancies, and their website (http://www.toyoko-inn.com/eng/) is excellent.
Western-branded hotels are rare outside Tokyo and Osaka; elsewhere, it's Japanese brands like JAL/Nikko (http://www.jalhotels.com), Rihga Royal (http://www.rihga.com/) and Prince (http://www.princehotels.com) that rule the roost. Full-service five-star hotels can turn pampering into an artform, but tend to be rather bland and generic in appearance, despite steep prices starting from Â¥20,000 per person not per room. However, there are several types of uniquely Japanese and far more affordable hotels: