A Visitor with a working-holiday visa who stayed for less than one year in Japan is basically treated as non-resident under the Income Tax Act.
When such a non-resident receives a salary in Japan, an income tax and a special income tax for reconstruction are withheld at the rate of 20.42%. And taxation for the non-resident is completed by paying this withholding tax. The non-resident cannot file a final tax return, so there is no refund of tax deducted from the salary.
In addition, if a non-resident received the salary from a Japanese company or a resident, it is not subject to tax exemption under the tax treaty.