Nato has withdrawn all its personnel from Afghan ministries after two senior officers were shot dead in the interior ministry building in Kabul.
Nato said an "individual" had turned his gun on the officers, believed to be an American colonel and major, and had not yet been identified or caught.
Nato commander Gen John Allen condemned the attack as "cowardly".
The shootings come amid five days of deadly protests over the burning of copies of the Koran by US soldiers.
The interior ministry was put in lock-down after the shootings, officials said.
The BBC's Orla Guerin in Kabul says eight shots were reported inside the building, which should be one of the safest in the capital, and that any Afghan who carried out the attack would have had the highest clearance.
Local media reports said the gunman was an Afghan policeman but this has not been confirmed.
The reports suggest the incident followed a "verbal clash".
Gen Allen said he condemned the attack, adding: "We will pursue all leads to find the person responsible. The perpetrator of this attack is a coward whose actions will not go unanswered."
He said: "For obvious force protection reasons, I have also taken immediate measures to recall all other Isaf personnel working in ministries in and around Kabul."
But Gen Allen added: "We are committed to our partnership with the government of Afghanistan to reach our common goal of a peaceful, stable and secure Afghanistan in the near future."
Isaf spokesman Brig Gen Carsten Jacobson said that Nato could not yet reveal the identity of those killed.
He also said: "We cannot confirm where the killer came from, what his nationality was, whether he was in uniform or not, all these questions are not known."
Early reports suggest the two officers were shot in the ministry's command and control centre.
The BBC's Bilal Sarwary in Kabul says this is where representatives of 34 provinces meet to plan security.
He quotes sources as saying that Interior Minister Bismullah Khan was having a meeting with senior Western officials elsewhere in the building when the shooting took place.
The Taliban said in a website statement that it carried out the attack in response to the Koran burnings.
But Gen Jacobson would not be drawn on any link to the protests.
He said: "We have seen an emotional week, we have seen a busy week - but it would be too early to say this incident was linked."
He added: "It is very regretful to see the loss of life again on this day, and that includes the loss of life that we have seen around demonstrations."
Angry protests over the burning of the Korans continued on Saturday, with a UN compound in the city of Kunduz set alight.
Four people were killed and dozens injured in clashes in the city, according to local doctors. Three more people were killed in the southern province of Logar.
The governor's house in Laghman province also came under attack on Saturday and there were demonstrations in Paktia, Nangarhar and Sari Pul provinces.
Nearly 30 people have died since the protests began on Tuesday.
US personnel apparently inadvertently put the books into a rubbish incinerator at Bagram air base, near Kabul.
US President Barack Obama has apologised for the Koran-burning incident.
In a letter to his Afghan counterpart Hamid Karzai, Mr Obama said the books had been "unintentionally mishandled".
Muslims consider the Koran the literal word of God and treat each book with deep reverence.----
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In: World News, Afghanistan
Tags: muslim, afghan, mad, koran, burnt, NATO, officers, killed, ministries, pullout, afghanistan
Location: Afghanistan (load item map)
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