In 1936, following the recommendation of the Moseley Royal Commission and the subsequent amendment of the Aborigines Act 1905, functions of the Aborigines Department were considerably increased and its name was at the same time changed to that of the Department of Native Affairs.

In 1947, the portfolio of the Minister for Native Affairs was created and a year later the Bateman Survey recommended drastic changes in the organisation of the department. These changes were duly carried out in the following year.

In 1954, the name of the department was changed to the Department of Native Welfare and its duties and functions were laid down by the Native Administration Act of that year.

This department had control of Aboriginal affairs for the area above latitude 25 degrees South in Western Australia. The Department of Fisheries had control of Aboriginal affairs for the area below latitude 25 degrees South in Western Australia.

Auber Octavius Neville was appointed Chief Protector of Aborigines on 7 May 1915. He became Secretary for the Department of the North West on 1 November 1920, combining this position with that of Chief Protector (North of the 25th parallel). When the Aborigines Department was re-established in 1926, Neville became once again, on 30 June 1926, the Chief Protector of Aborigines for the whole State.

In 1909, the Aborigines and Fisheries Departments were amalgamated into one agency, the Department of Aborigines and Fisheries. This was partly due to financial constraints and partly due to the expediency of running as one the two departments whose interests lay mainly in the northern part of the State.

After World War I, the Department was abolished and its functions pertaining to Aboriginal affairs south of the 25th parallel, as well as to fisheries throughout the State, were taken over by the Fisheries Department.

Charles Frederick Gale was appointed the second Chief Protector of Aborigines on 1 October 1908. He undertook this position together with that of the Chief Inspector of Fisheries. In 1911, Frederick Aldrich was appointed Chief Inspector of Fisheries and Gale's duties were limited to that of Chief Protector of Aborigines. Gale was dismissed from office in 1915 at an age of 54, ostensibly as an "excess officer" and was vindicated by a Royal Commission appointed to inquire into his dismissal.

Auber Octavius Neville (Secretary of the Immigration Department since 1911) was appointed as Gale's successor on 7 May 1915.

The 1897 Aborigines Act established the first Aborigines department in Western Australia. The department started to function in April 1898, as a sub-department of the Treasury, with a small staff, a permanent head called the Chief Protector of Aborigines, and a statutory grant of 5 000 pounds. In 1901, the department was assigned to the Premier's Department, a year later to the office of the Colonial Secretary, and in 1905 its control was transferred to the Minister for Commerce and Labour. About the same time, as a result of a Royal Commission appointed in 1904, it was raised to the status of a department and allocated a minmum statutory grant of 10 000 pounds.

In 1909, the Aborigines and the Fisheries Departments were amalgamated into one agency; the Aborigines and Fisheries Department. This step was due partly to a policy of financial stringency on the part of the government and partly to the expediency of running as one the two departments whose interests in that period lay mainly in the northern part of the State.

The first Chief Protector of Aborigines was Henry Charles Prinsep (who was formerly Under-Secretary for Mines). Prinsep's appointment commenced on 1 April 1898 but was without any legal authority (see the 1904 Roth Royal Commission, question 207). The Aborigines Act 1905 legalised the situation and his appointment was re-gazetted on 4 May 1906.

Charles Frederick Gale was appointed Acting Chief Protector of Aborigines during Prinsep's absence commencing 11 December 1912. Gale was appointed Chief Protector of Aborigines and Chief Inspector of Fisheries on 1 October 1908.