Salaries paid to non-residents of Japan are subject to Japanese withholding tax. So, if you are an employer in Japan and you are paying a salary to non-residents, you are required to withhold 20.42 percent of the salary as an income tax. This amount has to be paid to the government the following month.
If you miss the payment deadline you may have to pay an additional 5-10 percent penalty.
As a non-resident you are not required or permitted to file a tax return in Japan. That means you cannot claim any expenses or deductions and that you will have to pay a 20.42 percent income tax.
A typical situation is when a company hires people who have come to Japan with a working holiday visa. This is common in ski resort areas.
These people typically live in a hotel for a few months while they are working and then leave Japan when the ski season is over. Employers still need to deduct 20.42 percent of their salary.