Two Americans who were shot dead inside the inside the heavily barricaded interior ministry in the centre of Kabul today are believed to be a colonel and a major in the US military.
The interior ministry said in a statement that two "foreign partners" had been killed.
The ministry has been sealed shut and no one is allowed in or out, security sources said.
The Afghan Taliban claimed responsibility for the killings saying the shootings were in retaliation for the burning of copies of the Muslim holy book at a Nato base.
Nato's top commander in Afghanistan, General John Allen, said he was recalling all staff working at ministries in the Afghan capital in the wake of the killings.
"For obvious force protection reasons, I have also taken immediate measures to recall all other ISAF personnel working in ministries in and around Kabul," Mr Allen said in a statement.
Four people were shot dead by Afghan security forces as protests over the burnings of the books raged for a fifth day.
The burning of the Korans at the Bagram compound this week has deepened public mistrust of Nato forces struggling to stabilise Afghanistan before foreign combat troops withdraw by end 2014.
Despite an apology from US President Barack Obama over the burning of the Koran and a call for restraint from Afghan leader Hamid Karzai, thousands took to the streets after 12 people were killed and dozens wounded yesterday, the bloodiest day yet in demonstrations.
A protester was shot dead in Logar province south of Kabul after hundreds of protesters, many chanting "Death to America!" - a slogan heard at protests throughout the week - charged at police. Two people were wounded.
In the restive northern Kunduz province, two protesters were shot dead by Afghan security forces as they set alight shops and buildings, senior police detective Ghulam Mohn Farhad told Reuters. Several people were wounded.
Twenty people were wounded when demonstrators hurled stones in eastern Laghman province, health official Abdul Qayumi said.
The capital, Kabul, was calm, with police and security forces deployed across the city.
Muslims consider the Koran to be the literal word of God and treat each copy with deep reverence. Desecration is considered one of the worst forms of blasphemy.
The Koran burnings underscore the deep cultural divide that still exists more than 10 years after US troops invaded to oust the Taliban and have deepened public mistrust of the West.
The protests could dent plans for a strategic pact that Washington is considering with Kabul, which would allow a sharply reduced number of Western troops to stay in the country, well beyond their combat exit deadline.