The foreign company has a duty to pay corporate tax if the company has a domestic income source from investing domestic real estate or running a company inside Japan.
A taxation method, the tax rate are determined by such as income tax law or Corporate Tax Law (it is said with “a civil law” as follows) , but a different decision may be formed about a taxation method or an application tax rate by a tax convention. In this case the rule of the tax convention has priority over the rule of the civil law and is applied
But all is not applied to the rule of the tax convention automatically. As an example, it is necessary to submit a report book to a taxation office when a foreign country corporation receiving payment of domestic source income targeted for withholding taxes is going to receive reduction or an exemption based on a tax convention about income tax withheld in Japan.
When you do not submit this report book, you cannot receive the reduction based on the tax convention or an exemption.
However within the five years after you paid tax, if you submit the report to your district tax office, you are able to request a claim for a refund of the balance of reduction or exemption and the tax which taxed by a civil law.
You should check a tax conventions and the amount of withholding tax again and ask a tax professionals.
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