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Work on the construction of the Alfred Graving Dock commenced in 1864. No expense was spared in its construction and it represented the greatest single work undertaken by the Victorian Government since separation from New South Wales. When completed the dock allowed for effective underwater repairs to damaged ships to be undertaken in Victoria and it was then no longer necessary for ships to go to Sydney for such repairs. The Dock was constructed under the supervision of the Public Works Department. The dock's memorial stone was laid by Prince Alfred Duke of Edinburgh and in 1874 the first vessel entered the dock.
In 1913 the Alfred Graving Dock was taken over by the State Shipbuilding Yards and in 1917 the yards were acquired by the Commonwealth Government. In 1924 the dock was purchased by the Melbourne Harbor Trust who remained in control until 1942 when it was acquired by the Royal Australian Navy and administered as part of the Williamstown Naval Dockyard.