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In Japan it would not be uncommon for people to pay with cash (more people use cash in Japan anyway), anyway, either credit or cash, all is usually paid upfront at check-in. There is generally no predeposit then the rest paid at check out, generally you just pay all at check-in.

Some small hotels ask that you pay up front the fees for the 3 days you would be staying. Upon check in, you can ask to prepay the room. If there are incidentals such as beverages, you can pay for those when you check out. Some small Japanese hotels do not have a mini bar in the room so there are no incidental charges to accrue.

My company has a similar situation. I have found it increasingly difficult to pay for hotels with cash. In this regard the financial world has gone mad! In fact many hotels will not accept cash period. In a few cases like in NYC where nearly all hotels require a credit card, I have had to stay at a motel 6 in New Jersey because no matter how much $ you have no one else will rent you a room in that area. Seattle is a bit more relaxed, though you may need to stay at a less upscale place to use cash.

Like everyone has said, have enough credit in your credit or debit card so that deposit can be taken without any problems. The charges in each hotel varies so best to go to their site and read up on the small print. Always carry cash (any leftover and be reconverted) and cards - as backup with you

The amount varies depending on the rate that a hotel charges.

That said, if they do not have your credit card on file, it is customary to pay your entire stay upfront upon check in.

If you did not bring your credit card, they cannot charge your card obviously.