The Royal Australian Navy has stood aside the commander of one of its largest ships while it investigates an on-board complaint from a female officer.

Key points: The Royal Australian Navy is investigating a number of incidents on board HMAS Success

The Royal Australian Navy is investigating a number of incidents on board HMAS Success Commander Michael Letts has been stood aside during the investigation

Commander Michael Letts has been stood aside during the investigation In 2009 HMAS Success was found to have a 'predatory culture'

Commander Michael Letts has been temporarily replaced at the helm of HMAS Success by Captain Justin Jones, the ship's former commander, who retired in May this year.

Defence is also examining separate claims that two other crew members from HMAS Success bashed a man unconscious during a port visit to Malaysia last month.

"The Commanding Officer has been temporarily stood aside from Command whilst an investigation is underway into a number of incidents on board HMAS Success", the Defence Department said in a statement to the ABC.

A Defence source says the female officer lodged her complaint about Commander Letts after a late-night drinking session inside the ship's wardroom while it was visiting Singapore in August.

The second alleged incident involves the bashing of a civilian logistics agent who was contracted to Defence.

It's believed the man was left unconscious at the Port of Penang following an altercation with two crew members of HMAS Success.

Defence says both incidents remain under formal investigation.

"The investigation commenced as soon as Navy command became aware", the Department said.

"While the investigation is underway, it would be inappropriate to make further comment. All those involved have been given appropriate support and have received procedural fairness."

HMAS Success hit the headlines in 2009 after a tour of Asia where the ship was found to have a "predatory" culture and high levels of alcohol consumption.

In 2011 a Commission of Inquiry launched by the Defence Department found the source of much of the misconduct was the Marine Technicians (MT) unit, which had a "culture of silence and mutual protection".

Members of this unit put a bounty on a female crew member, collaborated to avoid random alcohol testing, and verbally and physically intimidated those who tried to speak out.

The author, Roger Giles QC, said the command structure failed to discipline transgressions properly, saying "the lack of action was known to other members of the crew and added to the perception that the MT sailors were a protected species".