Australian Special Forces in Afghanistan.

Australian special forces in Afghanistan.

Australian special forces are suspected of causing the deaths of two civilians - a six-year-old boy and his father - during a controversial night-time raid in Afghanistan last month.

The Afghans were found dead under a bullet-riddled blanket in a house next to the raid's target, in the district of Bulagh, to the west of Tarin Kowt, the capital of the south-central province of Oruzgan, on September 27.

The boy's body was allegedly found with a syringe stuck in his chest, as though someone had attempted medical care. He was lying on the chest of his father, a farmer, who had been shot in the neck and head.

The Defence Department confirmed to Fairfax Media on Wednesday that it was investigating the ''possible civilian casualty incident'' in Afghanistan.

A defence spokesman said the government of Afghanistan and International Security Assistance Force headquarters was informed of the incident but he declined to comment further.

Locals allege the father and son died when Australian soldiers fired down through a roof into the home, next to the property where an insurgent was hiding.

The incident is the third this year in which juveniles have been injured or killed during partnered raids - tactics that have been heavily criticised by Afghans.

The latest killings occurred about 8pm. During the raid, neighbours heard shouts that someone

had been shot. When they entered the house after the Australians had left, they found the bodies. Australian forces were reported to have paid compensation, but relatives are furious.

Despite a draw-down of regular Australian troops, civilian casualties continue to mount in the province as Australian special forces and paramilitary Afghan police conduct the controversial partnered patrols.

Earlier this year, Fairfax Media revealed how a father was gunned down in front of his daughter, who was also shot in the arm, as they rode on a motorbike near a partnered operation in Oruzgan. The Defence Department's explanation for the shooting was that the father had been riding the motorcycle in a manner consistent with an insurgent.

Questions have also been raised about an incident in June when a man, said to be a civilian and working in a field, was shot dead during a raid near Tarin Kowt.

On February 28, two boys were killed during a patrol in north-west Afghanistan. Australian troops were not thought to have fired the fatal shots.

A Senate estimates brief for the period from 2008 to May 17, 2013, reveals that 17 incidents occurred resulting in allegations of death or injury to Afghan civilians.

rcallinan@fairfaxmedia.com.au