Those exchange rates are insane! Five or six percent would be reasonable, but what you found was horrible. It sounds like using the ATM is the best way to go or just pay by card. That's the way I like to do things when travelling, but you always have to have some cash no matter what.
Having never been to Japan I couldn't personally comment on their currency exchanges. I just know everywhere else I've travelled I've never paid that high a rate except maybe inside an airport(which is always a rip off!)
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Big currencies like dollars and euros do not have these problems. I faced similar issue last year with getting Turkish Lira. Thankfully there are couple of money exchanges near my home so there is competition between them as well, in that I can sometimes get best rates.