A secret inquiry into alleged war crimes by Australian special forces is in its final stages, and is focusing on accusations of unlawful killings and the cruel treatment of civilians and former enemy fighters.

Key points: The secret inquiry has been running since May 2016

The secret inquiry has been running since May 2016 Members of the Defence community are annoyed at how long the investigation is taking

Members of the Defence community are annoyed at how long the investigation is taking The Inspector General of the Australian Defence Force says the probe is in its final stages

Investigators are looking into 55 separate incidents of alleged breaches of the rules of war in Afghanistan between 2005 and 2016.

A total of 336 people have given evidence to the probe so far.

The inquiry, by the Inspector General of the Australian Defence Force (IGADF), has been underway since May 2016 and was sparked by allegations and rumours of special forces troops killing unarmed Afghan men and children.

Members of the Defence community have been frustrated at how long the inquiry has been taking to complete.

The latest update was contained in the organisation's annual report for 2018-2019, which was only tabled in the Senate today despite being signed by Inspector General James Gaynor in November last year.

It said the investigation was aimed predominately at "unlawful killings of persons who were non-combatants or were no longer combatants, but also 'cruel treatment' of such persons."

"The Inquiry is also examining incidents relevant to the organisational, operational and cultural environment which may have enabled the alleged Law of Armed Conflict breaches," it said.

"The Inquiry is not focused on decisions made during the 'heat of battle'.

"Rather, its focus is the treatment of persons who were clearly non-combatants or who were no longer combatants."

The secretive probe is being led by former New South Wales Supreme Court Justice Paul Brereton, who travelled to Afghanistan last year to interview witnesses along with Australian Federal Police officers.

The Inspector General said the length of the investigation was caused by its complexity.

"Most other inquiries commence following specific allegations where not only the incidents and events themselves, but also potential witnesses, are known or can be easily identified," the report said.

"The starting point for the IGADF Afghanistan Inquiry — vague rumours of Special Forces soldiers' very serious wrongdoing over a period of more than 10 years — was much less well-defined."

Defence Minister Linda Reynolds said she expected the inquiry's final report to be delivered in the next few months.

"The ADF is well known and highly respected around the world for its exemplary standards and its insistence on them," she said.

"Where there are serious rumours and allegations raised about the conduct of our ADF members, Australians would rightly expect that they are thoroughly examined according to the rigorous and well-established processes in place.

"Australians would also expect that ADF members are treated with utmost fairness throughout these processes."

Shadow Defence Minister Richard Marles said it was inappropriate to comment on the investigation, as it was still underway.

"Labor supports this independent inquiry, it is essential we have confidence that our special forces are operating in a professional and legal manner," he said.