In the late 19th century, as the economy was shifting, Wisconsin's farmers began to raise concerns that the property-based tax system placed a disproportionate burden on them while many newer industries and corporations were able to escape taxation by hiding their property in other financial instruments.

[3] The Legislature responded to their report and the Tax Commission was reauthorized for another ten years, with a mandate to investigate and supervise the state taxation system (1899 Wisconsin Act 206).

Finally, in 1905, the Tax Commission was made a permanent entity of state government, with three commissioners each appointed to eight-year terms.

[3] In 1939, a major reorganization under Governor Julius P. Heil converted the previous three-member Tax Commission into a Department of Taxation headed by a single commissioner, while creating the separate entity known as the Wisconsin Tax Appeals Commission, now attached to the Wisconsin Department of Administration.

In addition, they administer state shared revenue and property tax relief payments to local governments.

Subdivisions include: Separate from the ordinary organizational structure of the Department, there are a number of specific commissions created by acts of the Wisconsin Legislature to oversee, advise, or administer certain functions.