A former sailor, who asked to be identified only as Bridget, said other sailors told her young men aboard the HMAS Ballarat frigate had been anally penetrated with water bottles and markers.
"People were set upon by members and stripped off and had things essentially put in their bums," she said.
Bridget said she and her friends in the navy wanted to report the incidents because "I think people are scared."
"If it happened in a normal workplace, the police would be called, charges would be laid," she said.
"Allegations such as these are serious and it is critical that the investigative process is properly followed. As such I will not speculate on any aspect of the allegations," said navy chief Vice Adm. Ray Griggs. "We have dealt with the allegations swiftly and I reiterate that inappropriate behavior is not consistent with our values and is not tolerated in [the] navy."
The Australian Broadcasting Corp. said the guided missile frigate is taking part in Operation Resolute, a border protection strategy, though its precise location wasn't reported.