The ADF has confirmed an industrial incident at HMAS Creswell last week.
A truck crane toppled over onto its side on one of the wharfs, leaving the boom arm in the water of Jervis Bay.
A spill containment boom was set up as a precaution against an oil of fuel spill.
There were no reports of injury.
The matter is being investigated by the Government Work Health and Safety Agency, Comcare.