In November, sailors aboard HMAs Ballarat exposed initiation rites which involved having senior sailors inserting pens and carrots in young sailors' behind.

On Wednesday, Service Police from an Australian Defence Force Investigative Service (ADFIS) announced that the department is making substantial progress with their investigation surrounding the controversy.

The investigation being conducted was that of a civilian criminal investigation process and all proofs and testimonies are now under prosecutorial review.

However, Defence decided that all information surrounding the investigation will remain classified and not for public consumption. What the department can only do is to give assurance that its doing all rightful and lawful process to come up with a sound decision.

Rest assured three members of the Ballarat ship were already suspended and upon the conclusion of all investigations, Defence may lay charges and refer the case to the Registrar of Military Justice for consideration by a Service Tribunal. The case may also be referred for civilian prosecution.

On the other hand, the Chife of Navy, Vice Admiral Ray Griggs, said that there will be a separate administrative inquiry involving broader procedural or cultural issues violated by the sailors involved.

"I am very keen to remain as open and transparent as possible without compromising the investigative process. Due to the serious nature of these allegations, maintaining the integrity of the investigative process remains my principal concern. Navy does not tolerate unacceptable behaviour. It is inconsistent with its values and the behaviours. Unacceptable behaviour by individuals damages our people and our effectiveness to conduct operations and achieve our mission," Mr Griggs said.

On Nov 6, Mr Griggs expressed admiration to the sailors who were braved enough to expose such inappropriate behaviour.

"The allegations were raised on Monday by one of our sailors, the matter was quickly reported through the chain of command for further investigation," Mr Griggs said.

"I applaud any member of the Navy who has the courage to raise concerns like these and I encourage anyone who is aware of, or who experiences, unacceptable behaviour to do the same. The alleged behaviours are simply not consistent with Navy values. Navy does not tolerate inappropriate behaviour and will act accordingly if any of the allegations are substantiated."