DEFENCE force chief General David Hurley has offered his condolences to the families of two boys killed during an incident involving Australian soldiers in Afghanistan.

But General Hurley says it is ''premature'' to determine how the incident occurred or who was responsible.

Defence is working with the NATO-led International Security Assistance Force (ISAF) and Afghan authorities to determine the facts surrounding the deaths in northwestern Oruzgan province on Thursday.

Australian soldiers from the Special Operations Task Group were conducting a routine liaison patrol when the incident occurred, General Hurley confirmed in a statement today.

''We deeply regret that the International Security Assistance Forces were responsible for the unintended death of two young Afghan boys during the operation,'' he said.

Australian personnel immediately reported the incident to Afghan government officials and military leaders in Oruzgan.

General Hurley said Defence takes the issue of civilian casualties very seriously, and soldiers operate under a strict set of rules to minimise unintended deaths and injuries.

Defence said no more details would be released while the incident was under investigation.

Officials said soldiers in southern Afghanistan shot the children, aged seven and eight, while tending livestock.

The tragic incident happened while Australian soldiers fought back after a Taliban attack in Oruzgan province, provincial governor Amir Mohammad Akhundzada told AFP overnight.

''The children were killed by Australian troops, it was a mistaken incident, not a deliberate one," Mr Akhundzada said, adding that insurgents had first shot at a helicopter carrying Australian soldiers.

Opposition Leader Tony Abbott said civilian deaths in war were ''absolutely tragic''.

''The horrible feature of war, one of the reasons why we should never lightly wage war, is that almost inevitably awful mistakes like this happen,'' he told reporters in Sydney.

Prime Minister Julia Gillard had been briefed on the matter, while parliamentary secretary for Defence David Feeney said he was aware of the allegations of civilian injuries but had no particulars.

When asked about the incident today, Ms Gillard said she wouldn't be making any comments.

''I'm not going to deal with the details of the incident in question. The CDF (Chief of Defence Force) will be making a statement later today,'' she told reporters in Sydney.

The incident is likely to escalate tensions over the conduct of international troops.

Civilian casualties caused by NATO-led forces have been one of the most contentious issues in the campaign against Taliban insurgents, often triggering widespread public anger and harsh criticism from President Hamid Karzai.

NATO's International Security Assistance Force (ISAF) expressed its "deep regret" over the children's deaths and said it remained committed to minimising civilian casualties.

"I offer my personal apology and condolences to the family of the boys who were killed," General Joseph Dunford, commander of ISAF, said in a statement.

"I am committed to ensuring we do the right thing for the families of those we harmed, as well as for the community in which they lived. We take full responsibility for this tragedy."

ISAF said the troops had opened fire at what they believed were insurgent forces.

It added that a joint Afghan-ISAF team visited the district of Shahidi Hassas in Oruzgan to investigate and meet with local leaders.

Last month, 10 Afghan civilians, including five children, were killed by a NATO airstrike in Kunar province.

Following the attack, Mr Karzai barred Afghan forces from seeking air support from foreign troops in a bid to curb civilian casualties.

Mr Karzai has regularly lashed out at senior ISAF leaders, demanding that civilian deaths must be avoided and saying the killings have worsened relations between his government and the international coalition.

Previous civilian deaths caused by ISAF forces, especially those involving children, have brought protesters onto the streets of Kabul chanting slogans against the presence of international troops in Afghanistan.

Security responsibility for Oruzgan, a restive province where Taliban insurgents have been holding sway, is being handed over to Afghan forces.

The bulk of Australia's 1550 troops are based in the province, and are focused on training and mentoring Afghan soldiers ahead of the withdrawal of NATO combat troops by the end of next year.

Originally published as ADF confirms death of two Afghan boys