The only time I had problems with using credit or debit cards in Japan was once when my bank slipped up and neglected to complete the steps for freeing up my credit card for overseas use. Oddly enough, the debit card from the same bank worked, fortunately enough to pay for my first night's lodging.

I immediately e-mailed my bank and got the hold lifted, along with replacement of the funds taken out of my checking account on the debit card.

Note that debit card withdrawal limits are based on 24-hour days in your home time zone. On one of my cards, the daily withdrawal limit is US$500. If I withdraw $300 at 7:00PM in Tokyo and try to withdraw another $300 at 9:00 the next morning, my card will be denied, because when Daylight Saving Time is in force, 7:00PM in Tokyo is 5:00AM in Minneapolis, while 9:00AM the next morning in Tokyo is 7:00PM the same day in Minneapolis.

It can be tricky to calculate, so try to make sure that your large withdrawals are at least 24 hours apart.