The majority of incidents being investigated by the inspector general of Australia's defence force's inquiry into the conduct of Australian special forces in Afghanistan relate to unlawful killings of non-combatants.
The investigation, which started in 2016, has heard from 338 witnesses, with new people continuing to come forward.
"At the end of the reporting period there were 55 separate incidents or issues under inquiry covering a range of alleged breaches of the Law of Armed Conflict, predominantly unlawful killings of persons who were non-combatants or were no longer combatants, but also 'cruel treatment' of such persons," the annual report of the Inspector General said.
Inspector General of the ADF James Gaynor said the inquiry was also investigating whether organisational, operational and cultural factors may have enabled the alleged breaches.
"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."
In the most expansive official update on the investigation, which is being led by Army Reserve Major General and NSW Supreme Court justice Paul Brereton, it was revealed the investigators are almost at the end of taking evidence, but the process has been slowed due to complexity.
Tracking "vague rumours of Special Forces' wrongdoing over a period of more than 10 years" was unlike most investigations into specific identifiable incidents of wrongdoing.
Mr Gaynor also said it had taken time for serving and former defence members to have confidence in the inquiry and whether senior leadership in Defence really did want to know if the rumours were true.
More witnesses had come forward as trust in the investigation had increased, leading to new lines of inquiry, or reinforcing existing lines of inquiry.
"During the reporting period and even now, some witnesses are only just becoming willing to make disclosures."
The investigation has five phases, which can happen concurrently. In the last financial year the focus moved to the final phase but new witnesses and lines of inquiry had affected the timetable.
Fourteen staff at the inspector-general's office were working on the case, and witnesses were being offered "a range of legal, psychological, medical, pastoral and social work support services."
The inspector-general's final report on the allegations will go to the Chief of the Defence Force, that will analyse whether there is enough evidence for each of their lines of inquiry.
Mr Gaynor also said it would "provide closure" Special Operations command and "for the many serving and former soldiers who have lived with concerns about the subject matter of these rumours for many years".
The investigation by the Inspector General is happening at the same time as an Australian Federal Police investigation into the alleged war crimes.
Officers for the AFP travelled to Afghanistan as part of the investigation last year.