In 1886, following the recommendation of a Select Committee, the administration of Aboriginal affairs was removed from the Colonial Secretary and entrusted to the Aborigines Protection Board, consisting of five members and a secretary, all of whom were nominated by the Governor without the advice or consent of the Executive Council. The establishment of the Board, although an important step, was in no way a radical departure from the existing administrative set-up and was brought about primarily by the increased pressure of business in the office of the Colonial Secretary. The Governor, and ultimately the Colonial Office (United Kingdom), remained responsible for matters of policy.

During the negotiations which led to the grant of responsible government in 1890, the Colonial Office insisted that the control of the Aboriginal people in Western Australia remained vested in the Governor even after the granting of self-government. Consequently, the Constitution Act of 1889 provided that the Aborigines Protection Board, rather than a government department under a Minister of the Crown, should remain responsible for the care of Aboriginal people and stipulated that the sum of 5, 000 pounds or 1% of gross revenue (should revenue exceed 500, 000 pounds per annum) be annually appropriated to the welfare of the Aboriginal population. It was also declared at the same time that the Governor, in directing the Board, should act independantly of his constitutional advisors.

These provisions, not unnaturally, resulted in friction between the Colonial Office and the Western Australian government, which objected to having to provide funds over which it had no control and regarded the continued existence of the Board as inconsistent with the spirit of self-government. Moreover, the Board had to rely on the executive for the carrying out of its orders and would be powerless to act should the government decide to block any of its decisions. The controversy, which was first brought into the open in 1891, lasted for almost six years and was finally resolved when complete control of Aboriginal affairs was passed to the government of Western Australia.