NATO has announced that all foreign advisers will be pulled out of their posts in Kabul.
The announcement came just hours after the shooting on Saturday of two International Security Assistance Force (ISAF) military advisers in the interior ministry in the Afghan capital.
Afghanistan's interior ministry said on Sunday that it suspects one of its employees may have killed the two officers.
"An employee has been identified as a suspect and he has now fled. The interior ministry is trying to arrest the suspected individual," read a statement e-mailed to the media.
President Hamid Karzai went on television to appeal for calm: "Now that we have shown our feelings it is time to be calm and peaceful."
Karzai "condemned with the strongest words" the treatment of Islam's holy book and said the perpetrators should be punished.
Al Jazeera's Bernard Smith, reporting from Kabul, said the withdrawal of hundreds of military and civilian advisers is a sign that NATO feels "no place is secure for any of their advisers" in Afghanistan.
In a statement, General John R Allen, ISAF commander, said that "for obvious force protection reasons, I have also taken immediate measures to recall all other ISAF personnel working in ministries in and around Kabul".
Speaking to Al Jazeera, Brigadier General Carsten Jacobson, ISAF spokesperson, said the adviser pull out was a necessary step to "account for all our personnel ... and bring them into their safe housing areas" in and around Kabul.
The two American soldiers were inside a room in the ministry's command and control complex used only by foreign advisers when they were killed. The only Afghans with access to that area are translators, Afghan officials said.
The interior ministry issued a statement confirming that two of the ministry's international advisers were killed and that an investigation had been launched.
Additional reports claimed the men were US military officers serving as ISAF trainers.
A statement issued by NATO said "initial reports indicate an individual turned his weapon against International Security Assistance Force service members in Kabul city today, killing two service members".
Our correspondent said ISAF had closed off access to their command and control centre where the two bodies were found.
Allen said the shooting would be investigated and all leads pursued "to find the person responsible". "The perpetrator of this attack is a coward whose actions will not go unanswered," he said.
In statements on their website and a Twitter account, the Taliban claimed responsibility for the shootings, which they say were in retaliation for Quran burnings at a US airbase.
Zabiullah Mujahid, a Taliban spokesman, identified the assassin as Abdul Rahman, adding that an accomplice in the ministry building helped him gain access.
Although official reports said two military advisers were shot, the Taliban, known to exaggerate tolls from attacks for which they take credit, claimed four high-ranking advisers were killed.
"After the attack, Rahman informed us by telephone that he was able to kill four high-ranking American advisers,'' Mujahid said.
In a post on his official twitter account, Captain John Kirby, a US defence spokesman, said there had been "lots of speculation on today's attack in Kabul; we do not know who killed ISAF members or why".
The shooting came on the fifth day of protests across the nation sparked by the burning of Qurans at a US base.
Hospital officials told Al Jazeera four protesters were killed and 34 wounded.
Three of the men were killed at a protest outside a UN compound in Kunduz province on Saturday morning, hospital officials said, adding that 30 other demonstrators were wounded in that protest.
The gathering had initially been peaceful, but turned violent after protesters threw stones at government buildings and the UN office, Sarwer Hussaini, a spokesman for the provincial police, said.
|Al Jazeera's Ghida Fakhry speaks to ISAF spokesperson about withdrawal of advisers
He said police had fired into the air to disperse protesters.
Denise Jeanmonod, a spokeswoman for UNAMA, the United Nations' Mission in Afghanistan, confirmed the incident, saying that the organisation was "assessing the situation at the scene".
Elsewhere on Saturday, one protester was killed and four others wounded during a protest in Logar province, south of Kabul, after hundreds of demonstrators took to the streets and clashed with security forces.
Protests also erupted in several other provinces on Saturday, with demonstrations reported in Sar-e-pol and Nangarhar provinces.
In Laghman province, a protest reportedly turned violent when an estimated 1,000 protesters threw rocks at police and attempted to storm the governor's house.
There were reports of casualties at that protest, but there was no immediate confirmation on the number of wounded.
On Friday, protests across the country led to the deaths of 11 Afghans, including a protester who was shot dead in Kabul. It was the deadliest day of protests since demonstrations began five days ago.
Brigadier General Carsten Jacobson, ISAF spokesperson, said the response to the protests was managed by "a police force that showed extreme skill and capability this week".