There are several types of accommodations available in Japan. If your budget is tight and come for business, you may find out ビジネス ホテル (business hotels) are reasonable and convenient. These are usually located near train stations or bus stops. But if you would like to enjoy traditional Japanese atmosphere, I strongly recommend to stay in 旅館 （りょかん：Ryokan) once.
Here is the example of 旅館
The 旅館 is a traditional Japanese style inn, sometimes located at an isolated place and in very quiet environment. They may have shuttles departure from airports or train stations to the accommodations. This is called 送迎 （そうげい：sougei: soh geh E) in Japanese.
You may find 民宿 （みんしゅく：Minshuku）as an accommodation by chance. This accommodation is generally small traditional Japanese accommodation which is carried out by a family and its relatives. Unfortunately, it may be relatively more expensive than 旅館; however, they may provide much fresh sashimi or seasonal food which are harvested or caught by themselves.
[The example link of 民宿]
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