James Martin, Stjepan Milosevic and Robert Poate.

James Martin, Stjepan Milosevic and Robert Poate. Photo: Reuters

An inquest on three Australian soldiers killed by a rogue Afghan soldier in 2012 will probe uncomfortable allegations about commander decisions and high-level army procedures, Fairfax Media has learnt.

In June, Queensland Coroner John Lock will hold an inquest on Lance Corporal Stjepan Milosevic, 40, Private Robert Poate, 23, and Sapper James Thomas Martin, 21, who were killed at the Patrol Base Wahabin in Oruzgan province on the evening of August 29.

Defence is believed to have engaged two barristers but has rejected a request to provide legal representation for the families of the dead soldiers on the grounds there is not enough funding, one source close to the case said.

The families of the men have declined to comment, not wishing to jeopardise any part of the inquest, but they are believed to be keen to see the role of senior leaders examined as opposed to low-level leaders who were in the front line at the patrol base.

One issue likely to be investigated by the coroner relates to the intelligence that was available about the threat of attacks by rogue Afghan soldiers at the time.

It is understood top-level commanders sent out orders two weeks before the attacks that warned of a high risk because it was the time of Ramadan, the holiest month in the Islamic calendar.

The orders, created around August 13, 2012, from Regional Command South, were sent to Command Team Oruzgan at the main base in Tarin Kowt. They were then supposed to be sent down the chain to the soldiers in the field.

The orders are understood to have warned of a heightened risk of green on blue attacks (Afghan on coalition forces).

It is believed, however, that the shortened version of these orders, which was transmitted from the Tarin Kowt-based task group to soldiers out in the field, has not been able to be obtained. Concerns about how commanders interpreted the orders are likely to be raised.

The attack took place several days after Ramadan - a scenario that low-level commanders may use as a reason for security not being upgraded.

Another issue likely to be raised is the location of the base's ''guardian angel'' - a soldier whose job it was to act as a sort of bodyguard for his fellow Australian troops while they were in the field with Afghan troops.

The guardian angel on the night was moved to a different position, away from where the three Australian soldiers died.

Sergeant Hekmatullah, the rogue soldier responsible for the attacks, was captured last year and jailed and has been appealing a death sentence.