Obama said the incident was not intentional and pledged a full investigation, a statement from the president's office said.
Obama’s statement follows a series of violent events.
An Afghan soldier killed two NATO troops earlier today, after opening fire on members of the U.S.-led International Security Assistance Force, the military said.
Taliban calls for revenge killings
ISAF did not identify the nationalities of the dead soldiers and gave no further details of the incident.
Asked whether the events were connected, an ISAF spokesman would only say: “There was a demonstration in the province.”
Afghan troops defending a foreign base in eastern Nangarhar province had “joined demonstrators and opened fire on foreign troops,” a protester told the Afghan Islamic Press news agency.
And in the morning, Taliban insurgents had urged Afghans to kill foreign soldiers in revenge for the burning of copies of the Quran, in a statement released to media outlets.
The militia called on Afghans to “not stop at protesting” but instead attack foreign troops.
“Kill them, capture them, beat them and teach them a lesson that they will never again dare to insult the Holy Quran,” it said in its statement.
“Since the protection of the lives and property of Muslims is the duty of all Muslims, protesters should target the invading forces and their installations,” the Taliban statement added.
However the Taliban’s main spokesman, Zabiullah Mujahid, told AFP that the Quran burning would not affect contacts with U.S. officials in Qatar, designed to build confidence and pave the way for a prisoner exchange. “We condemn the desecration of the Holy Quran in the strongest terms, but this issue will not affect this process in Qatar,” he said.
Anti-American protests against the burning of Qurans carried on for a third straight day, after nine demonstrators were shot dead and dozens wounded in violent protests yesterday, prompting Afghan President Hamid Karzai to urge calm.
Reuters reported that thousands of demonstrators rallied across the country on Wednesday, some chanting “Death to America!” and demanding U.S. and foreign military forces leave Afghanistan.
NATO has some 130,000 troops in Afghanistan supporting the government of President Hamid Karzai against an insurgency led by remnants of the Islamist Taliban regime overthrown by a U.S.-led invasion in 2001.