I'm in Europe and have ordered goods from Japan several times. I've always used EMS, they're cheaper than Fedex and the like and they don't charge their own fees for clearing customs, but I've always had to pay duties, fees, fleet, VAT and other charges. In this country (Spain) the overall expense to import something from outside the EU is about 30% of the declared value (including shipping cost). So declared value, and what you can produce as a payment receipt, or invoice, are the key items to estimate your customs cost.