The Harbour and Light Department was constituted in 1880 under the Chief Harbour Master, Fremantle. The Department was responsible for control of all maritime matters, including lighthouses and other navigation aids and the administration of the shipping and pilotage legislation. The Department controlled the ports of Albany, Vasse (Busselton), Bunbury, Geraldton, Port Irwin and Cossack and it operated lighthouses at Bunbury, Bluff Leading Light, Breaksea Island, Cossack, Fremantle, Point Moore, Port Irwin, Point King, Rottnest Island and Vasse. The Department passed control of Fremantle Port to the Fremantle Harbour Trust in 1903 and to Bunbury and Albany soon afterwards. Control of lighthouses was passed to the Commonwealth in 1915.

Following the passing of the Marine and Harbours Act 1981, the name of the Harbour and Light Department was changed to that of the Department of Marine and Harbours in 1982.

The Fremantle Harbour Trust was created under the Act of the same name in 1903. Certain functions of the Harbour and Light Department were transferred to the new body, particularly control of the pilotage service, signalmen and the Fremantle light keepers. A Board of Commissioners was responsible for carrying out the functions of the Harbour Trust as laid down by the Act. An Amendment Act in 1964 changed the name of the Trust to the fremantle Port Authority.

Under an amendment to the Fremantle Harbour Trust Act in 1964, the name of the Trust was changed to the Fremantle Port Authority.