A woman claims the "inappropriate behaviour" that prompted the navy to launch an investigation into sailors involved sexual assaults on young male sailors on HMAS Ballarat.
The Navy has confirmed the ship involved in the allegations is Anzac Class Frigate HMAS Ballarat, which is currently deployed on border protection operations.
Chief of Navy, Vice Admiral Ray Griggs, said the navy was being as open and transparent as it could within the limits of its investigation processes.
"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," he said in a statement on Thursday.
"We have dealt with the allegations swiftly and I reiterate that inappropriate behaviour is not consistent with our values and is not tolerated in Navy."
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
The woman who made the sexual assault claims is a former navy member who alleged younger male sailors were set upon and sexually assaulted by their crewmates.
"People were set upon by other members, stripped off and had things essentially put in their bums," the woman, identified only as Bridget, told Network Ten on Thursday.
In one instance, a sailor was left with a bleeding rectum after being anally penetrated by a whiteboard marker, she claimed.
Bridget said her friends still serving in the navy had asked her to get the truth out, because people were scared.
"If it happened in a normal workplace, the police would be called, charges would be laid," she said.
The Australian Defence Force opened a formal investigation on Tuesday after allegations against some members of an unnamed ship's company were made by a sailor.
However investigators will not be able to join the ship for several days.
HMAS Ballarat responded to a distress call from an asylum-seeker boat off the coast of Indonesia.
Australian Customs and Border Protection and the Australian Maritime Safety Authority could not comment on Thursday. The federal government is not scheduled to brief the nation on border protection until Friday.
However Indonesian search and rescue agency, BASARNAS, has confirmed to AAP that a distress call had been received from a vessel in the Sunda Strait earlier on Thursday.
The Indonesian spokesman said HMAS Ballarat had responded to the distress call from the boat.
