A group signal flag and pennants signalling the ship's number J244 are flown from the port side yard of the foremast. Two individual flags are also regularly flown when the ship is open for inspection.
The Australian National Flag—the Blue Ensign—is flown from the jack staff (at the bow).
It was flown when the ship was alongside or at anchor, and is raised or lowered in the same manner as the White Ensign. Protocols for flying flags at half-mast are observed.
From the formation of the Royal Australian Navy in 1911 until 1967 RAN ships flew the White Ensign. HMAS Castlemaine flew the White Ensign during her entire operational life. It is deemed appropriate to fly it now, as the ship is a museum ship and is not in commission.
In 1965, the Minister for the Navy informed The House of Representatives the Government was looking at variants of the white ensign which would be unique for Australian naval ships. In 1966 The Naval Board approved the design described as 'a white flag with the Union Flag in the upper canton at the hoist with six blue stars positioned as in the Australian Flag.' Royal assent to the new design was granted on 7 November 1966, and it was flown from all RAN ships from 1 March 1967.