In order to respond to the confusion in the tax administration after World War II, the Government separated the tax enforcement aspect from the duty of the Tax Bureau of the Ministry of Finance, which had undertook increasingly excessive operations, and established the National Tax Agency in 1949, as an administrative agency in charge of assessment and collection of Internal taxes (excluding customs duty, tonnage due and special tonnage due). Thus, a systematic tax administration structure, comprised by the National Tax Agency, Regional Taxation Bureaus and Tax Offices, was established.

Today, the National Tax Agency consists of the Head Office, 11 Regional Taxation Bureaus, the Okinawa Regional Taxation Office and 524 Tax Offices.