A two-year-long investigation has uncovered numerous concerns about the conduct of Australian special forces in Afghanistan, including several incidents of possible unlawful killings.

Key points: Supreme Court judge has been examining claims of illegal actions by members of SASR, Commando units

Supreme Court judge has been examining claims of illegal actions by members of SASR, Commando units Sources expect cases will be highlighted where suspected homicide could be referred for further investigation

Sources expect cases will be highlighted where suspected homicide could be referred for further investigation It is not clear which authority could be asked to determine what, if any, further legal action could be taken

Since May 2016, New South Wales Supreme Court Judge and Army Reserve Major General Paul Brereton has been examining claims of illegal actions during the 12-year conflict committed by members of the Special Air Services Regiment and Commando units.

Justice Brereton is helping the Inspector General of the Australian Defence Force (IGADF) as he conducts a secretive and sweeping inquiry into Australia's elite troops, including possible breaches of the Geneva Convention.

Several high-level sources in the Defence community have confirmed to the ABC that Justice Brereton is nearing the end of his work and is soon expected to highlight a handful of cases where suspected homicide could be referred for further investigation.

It is not known what incidents the concerns relate to, but sources have told the ABC that five cases involving alleged unlawful killings have been uncovered.

The ABC approached the IGADF for comment on its expected findings but was referred to the Defence Department.

In a statement, Defence Chief and Air Chief Marshal Mark Binskin stressed that "serious allegations" from the Afghanistan War must and are being "thoroughly examined independently from the chain of command".

"To protect the integrity and independence of the inquiry, it [is] essential that we follow due process and avoid any speculation on what the inquiry may or may not find," he said.

"I have requested that the Inspector General complete this inquiry as soon as possible, however it is important to see the IGADF Inquiry through to conclusion — without interference or influence".

Future legal course unclear after report's release

As the Australian Defence Force prepares for the release of the IGADF's report before the end of the year, it is not clear which authority could be asked to determine what, if any, further legal action could be taken against any individual soldier.

Justice Brereton is helping conduct a sweeping inquiry into Australia's elite troops. ( RSL Veterans' Centre )

Defence figures believe Australian Federal Police often struggle to investigate war crimes outside Australia, and it is not clear whether cases would be referred to the Commonwealth Director of Prosecutions, or the military prosecutor.

Last night Veterans' Affairs Minister Darren Chester told the ABC's National Wrap program that the IGADF would make recommendations to the Government when its report was completed.

"I just want to stress that the process here is important, that it gets followed through properly, that the allegations are properly investigated and if it's required that action needs to be taken, the Government will take that report very, very seriously," he said.

However, the Minister said he could not say if the AFP would investigate any eventual criminal findings because the IGADF had not yet released its report.

"We're not aware yet what the findings are going to be from the Inspector General's report … if there are findings of criminality than there could be quite significant consequences," he said.

Mr Chester also acknowledged that the IGADF process could be having an impact of veterans who served in Afghanistan.

"It's important that we do support them because obviously if there's going to be serious allegations made, it may impact on their wellbeing having been former members," Mr Chester said.

"So it's important that we reach out to them and make sure that support is available to them if indeed they require that support."