For foreign companies, the competent tax office is the location of the main permanent establishment in Japan.

The National Tax Agency , an external organ of the Ministry of Finance, is in charge of the assessment and collection of internal taxes. It supervises 12 Regional Taxation Bureaus throughout Japan, under which 524 local tax offices are set up to execute tax administration. (NTA)

Taxpayers are required to file returns and pay for internal taxes such as Corporation tax, Business taxes and Consumption tax to the tax office with jurisdiction over the location where the taxpayers reside.

Local taxes are administered by the Local Tax Bureau, which is responsible for planning local taxes on the prefectural and municipal levels and for determining competent tax authorities. Public services regarding tax assessment and collection are provided by the local governments, which have the right of taxation. The Bureau of Taxation, taxation sections, etc., under each prefecture and municipality (city, ward, town, or village) are in charge of the assessment and collection of prefectural taxes and municipal taxes, respectively.