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.

As well as the State's fisheries, this department had control of Aboriginal affairs for the area below latitude 25 degrees South. (The Department of the North West had control of Aboriginal affairs for the area above latitude 25 degrees South).

The Fisheries Department was a sub-department of the Colonial Secretary's Office (1920-1924), the Chief Secretary's Department (1924-1932, 1949-1953) the Premier's Department (1933-1938), and the Department of the North West (1939-1948) until 1953 when it achieved the status of a separate department.

In 1964 the growing importance of the Department's fauna conservation activities was acknowledged by a change of name to the Department of Fisheries and Fauna.

As well as the Fisheries Act, the Department administered the Game Act, the Fauna Protection Act and the Wildlife Conservation Act.