A raid to find the man who killed three Australian soldiers was by the book, Defence Minister Stephen Smith says.
The mission - which saw two Afghans killed - has been condemned by Afghan President Hamid Karzai as a "unilateral operation."
But today, Mr Smith told reporters the mission was properly authorised and that both Afghan and Australian sources have confirmed that the two men killed were insurgents.
Yesterday Mr Karzai said that the deceased men - reported to be tribal elder Raz Mohammad Khan, aged between 50 and 70, and his son, Abdul Jalil, 30 - had "no relationship with the government or the militants" and condemned the mission as a "unilateral operation".
Mr Smith explained that there had been a "misunderstanding" between the Afghan government and Australia on the matter."We're disappointed that there is a misunderstanding but I don't put it any higher than that," he said.
Mr Smith said Australia's ambassador to Afghanistan had already been in contact with the palace in Kabul to clear up the differing accounts.
''We have made our view to the palace crystal clear," Mr Smith said.
Mr Smith also confirmed that the operation was authorised by Afghan authorities and was conducted within the "usual and normal procedures".
"Any loss of life is of course regrettable," he said.
Mr Smith said it involved about 60 Australian personnel and 80 Afghan soldiers.
Labor MP Mike Kelly - who was an army colonel before entering politics - said Mr Karzai's comments had been made in the context of a very emotional environment.
"You can understand why people may be on edge and may rush to judgment at times," he told Sky News.
Three Australian soldiers were killed in a so-called ''green on blue'' attack in their base in Oruzgan last week.
Lance Corporal Stjepan ''Rick'' Milosevic, Sapper James Martin and Private Robert Poate from the 3RAR Task Group were killed, and two other soldiers were wounded, when an Afghan sergeant, Hekmatullah, opened fire on them at Patrol Base Wahab in the Baluchi Valley region of Oruzgan province on Wednesday evening.
Mr Smith said 12 people, including a woman, had been detained during the raid. It was the first time a woman had been detained in such an operation, he said.
All had been released except one man, who was regarded as an ''insurgent leader''.
The Defence Minister said there was evidence the man had sought to assist or did assist Hekmatullah and International Security Assistance Force officials agreed with this analysis.
He said there had been no ill treatment of any of the detainees.
Mr Smith also said that even though ISAF hadsuspendedtraining police recruits in Afghanistan - to put in place extra vetting measures - Australia's operations were not affected.
''Australia does not train Afghan police at all so this has no impact on Australian operations in Oruzgan Province or Afghanistan generally,'' Mr Smith said.
He said that as of this morning, it would be business as usual for Australian troops, albeit with additional force protection measures.
ISAF has also announced that partnered operations between ISAF (which includes Australian personnel) and Afghan forces would continue. Special forces operations will also continue.