KABUL (AP) ― President Barack Obama apologized to Afghans on Thursday for the burning of Qurans at a U.S. military base, trying to assuage rising anti-American sentiment as an Afghan soldier gunned down two American troops during another day of angry protests.

The U.S.-led military coalition says the Muslim holy books were sent by mistake to a garbage burn pit at Bagram Air Field and the case is under investigation. The explanation and multiple apologies from U.S. officials have yet to calm outrage over the incident, which has also heightened tension between international troops and their Afghan partners.

Thousands of protesters, some shouting “Long live Islam!” and “Death to America!” staged demonstrations across Afghanistan for a third day. Protesters climbed the walls of a U.S. base in the east, threw stones inside and adorned an outside wall with the Taliban’s trademark white flag.

At other sites, demonstrators burned tires or American flags. Afghan police and international troops fired guns in the air to disperse the crowds.

The protests sparked clashes with Afghan security forces that left at least five demonstrators dead. A Norwegian soldier was wounded by a hand grenade hurled into a coalition compound.

On Wednesday, six people died in protests in Kabul and three other provinces.

The civil unrest comes at a time when Afghan President Hamid Karzai is trying to negotiate a long-term partnership agreement with the United States to govern the activities of U.S. forces in Afghanistan after 2014, when most foreign combat troops will have left or taken on support roles.

Karzai called for calm until an investigation is completed, but the incident highlighted the fitful and often strained relationship of the two nations.

White House press secretary Jay Carney told reporters aboard Air Force One that Obama’s apology to Karzai was “appropriate given the sensitivity” of the issue. He said the apology was part of a three-page letter to the Afghan leader. Presidential apologies are rare, but he noted that former White House press secretary Dana Perino apologized on behalf of President George W. Bush in 2008 after a U.S. serviceman shot a Quran.

Tommy Vietor, a spokesman for the National Security Council at the White House, said Obama’s letter, which addressed issues being negotiated in the partnership document, was delivered by Ryan Crocker, the U.S. ambassador to Afghanistan. In the letter, Obama expressed “regret and apologies over the incident in which religious materials were unintentionally mishandled.’’ Vietor said

Karzai met Thursday with parliamentarians _ many of whom had been particularly vitriolic Wednesday in calling for Afghans to wage a holy war against international forces. The Afghan president told the lawmakers they were right to raise their voices against the desecration of Islam’s holy book, but said a government investigation was the appropriate way to handle the case, according to a statement issued by his office.

The statement said Karzai told the lawmakers that a U.S. officer responsible for the burning “didn’t understand’’ what he was doing and that the United States had “accepted the mistake of its officer.’’

The coalition said the investigation is still under way.

The unrest started Tuesday when Afghan workers at the sprawling American base north of Kabul noticed that Qurans and other Islamic texts were in the trash that coalition troops dumped into a pit where garbage is burned. Some Afghan workers burned their fingers as they tried to salvage some of the books. Afghan government officials said initial reports indicated four Qurans were burned.

The materials had been taken from a library at Parwan Detention Facility, which adjoins the base, because they contained extremist messages or inscriptions. Writing inside a Quran is forbidden in the Islamic faith, and it is unclear whether the handwritten messages were found in the holy book or other reading materials.

A military official said it appeared that detainees at the prison were exchanging messages by making notations in the texts.

A delegation of Afghan religious leaders, lawmakers and government representatives visited Bagram as part of the investigation. They issued a statement late Thursday calling for an end to protests and accused insurgents of infiltrating the gatherings to foment violence. They said they expected those responsible for the Quran burning to be prosecuted through the U.S. military court system.

The Taliban used the opportunity to incite more attacks on foreign forces. In a statement, Taliban spokesman Zabiullah Mujahid described the burning as an “unforgivable crime.’’ He urged Afghan army and police to become “real sons of the nation’’ by turning their guns on coalition forces.

Afghan authorities said demonstrations were staged inside the capital and in seven of Afghanistan’s 34 provinces.

The deadliest was held outside an American base in the Khogyani district of Nangarhar province in eastern Afghanistan. Two protesters were killed by Afghan police and an Afghan soldier turned his gun on American troops, killing two.