What is your de minimum for importing into Japan by post?
It is entirely possible that your seller did this for you, yes. It all depends on the value of the item, your country's de minimus, and the country of manufacture for the item being imported.
If I, for example, mailed you a $220 toy made in China, this is the breakdown of costs given to me by the Canada Post estimator.
Estimated Duties¤9.21¤720.12Estimated Taxes¤10.01¤782.74Total Estimated Duties and Taxes¤19.22¤1,502.86Shipping¤80.12¤6,265.33Total Estimated Cost¤99.34¤7,768.19
Convert to CAD and apply to your own circumstances at https://www.canadapost.ca/cpotools/apps/wtz/personal/findHsCode?execution=e1s11
Couriers follow a different system. Some may require pre-payment of duty.
Only you know the specific details of your transaction.
Or, the seller could be fudging it and keeping a handling fee that has nothing to do with duty paid.