During the early years of settlement the naval defence of Australia was provided by detached Royal Navy units of the East Indies Station , based in Sydney . However , in 1859 Australia was established as a separate squadron under the command of a commodore , marking the first occasion that Royal Navy ships had been permanently stationed in Australia . The Royal Navy remained the primary naval force in Australian waters until 1913 , when the Australia Station ceased and responsibility handed over to the Royal Australian Navy ; the Royal Navy 's depots , dockyards and structures were given to the Australian people .