Prime Minister Tony Abbott says allegations of sexual abuse on HMAS Ballarat are disturbing but has defended the conduct of most defence personnel.
"I think that the overall culture of our defence forces and of our defence personnel is an admirable one," Mr Abbott told reporters on Friday.
The defence force began formal investigations on Tuesday after allegations against some members of the ship's company were made by a sailor.
A former member of the navy later said officers were "set upon, stripped off and had things essentially put in their bums".
Mr Abbott said "all credible allegations of this kind of conduct are disturbing".
"I want to defend the overall conduct of defence personnel and I want to applaud the way our defence chiefs have taken a very strong stand on this issue," he said.
"I do think that our defence forces are determined to stamp out inappropriate behaviour."
He said most defence personnel had high aspirations and noble purpose.
Acting opposition leader Tanya Plibersek says the allegations must be "absolutely thoroughly investigated", noting the navy had done so with similar claims in recent years.
"I think there is culture change in the navy because of the increasing openness and encouragement to people to report allegations of abuse," she said.
The Navy confirmed HMAS Ballarat is the ship involved but declined to divulge the nature of the allegations.
HMAS Ballarat is on border protection operations and is believed to have been involved in the rescue of 56 people aboard an asylum-seeker boat in Indonesian waters on Thursday.
Investigators will not be able to join the ship for several days.
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