Although it takes more time than traveling by train, the fare is cheaper than train fares. It is not as comfortable as traveling by train either, but it can be a money saving on one-day accommodation as well as transportation cost.
To use long-distance buses, prior reservation is required in most of the cases. You can purchase tickets onsite at the bus station such as Shinjuku. Also, There are websites offering online-booking services for these types of busses, but, most of them are available only in Japanese, unfortunately. If you have no problem understanding Japanese language, the following websites will be convenient. You can book online and make the payment at a nearby convenience store ( or by credit card).
To find more info, the following web sites will be a great help
Shinjuku Expressway Bus Terminal
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Shinjuku Expressway Bus Terminal (SEBT)