In most big cities, usually in shopping areas near stations, you can find discount ticket shops, or kinken shoppu (金券ショップ), which sell, among other things, cheap airline and Shinkansen tickets. These shops buy up discount group tickets and sell them on individually, usually at around twenty percent cheaper than the regular prices. These are legitimate operations, but you’ll need to be able to read and speak some Japanese to be sure you’ve got the ticket you need, and there may be some days when travel isn’t allowed. With the Shinkansen tickets you can’t make seat reservations at a discount shop, so you’ll need to go to a JR ticket office to arrange these.

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