I think this is determined by your bank and the limits you agree to when you establish your account. Daily limits are typically $300. Doesn't matter where you make the withdrawl, Japan or your hometown grocery, the limit is the limit. Because I travel a lot internationally I have run into same issues that you describe, and I convinced my bank (Wells Fargo) to increase my daily limit to $500, but that's as far as they would go. They will not do temporary increases (say for the duration of a trip) either, stating it's for customer's protection as well as bank liability.

With the weak dollar now, and Euro at $1.34-1.35, even a $500 daily limit is really not a lot. I usually withdraw the max that I can (assuming I need that much and will be there long to spend it) so as to minimize impact of transaction fees (WF=$5.00 out of network ATM withdrawl fee).

I'd recommend asking you bank to increase your limit.