Did you use a Visa or MC to guarantee your reservation or provide a deposit? If so, the hotel may normally accept Visa/MC, but your card might have been declined if the hotel tried to submit a pre-authorization request.

We learned in checking with the issuers of our Visa/MC and ATM cards that each had different rules regarding transactions in Japan. One VISA issuer required notification prior to travel to Japan, otherwise all charges originating in Japan would be declined. Another informed us that signature-based transactions were fine, but PIN-based transactions were not. Interestingly, we don't have these issues when traveling to other countries. We were told that there is a high incidence of fraudulent charges originating from Japan, hence the extra security.