The process of withholding from employment income paid to residents is broadly divided into the process of withholding from monthly (daily) salary and bonuses, etc., and the year-end adjustment process at the end of the year. The key points to consider here are: (1) the scope of taxable employment income, (2) the requirements for the application of various deductions, such as exemptions for spouses and dependents, and (3) how to use the tax amount table and the methods for specific tax amount calculations.
(Note) The definitions of resident and non-resident are unrelated to nationality or residence (visa) status. An alien worker having a domicile in Japan or a continuous residence in Japan for 1 year or more is subject to withholding as a resident.
(上記 国税庁HPより引用)