KABUL, Afghanistan – Afghans enraged by the alleged desecration of Islam’s holy book at an American prison staged a third day of violent protests yesterday, burning an American flag in the capital and ransacking relief group offices to the south as demonstrations spread to neighboring Pakistan.

Secretary of State Rice promised “appropriate action” would be taken if the allegations are proven true.

Three more demonstrators were shot and killed in clashes with police, officials said, bringing the death toll to at least seven in the biggest anti-American protests in Afghanistan since the fall of the Taliban in 2001 – and presenting a fresh challenge to efforts to stabilize the country.

While most of the protesters were students, officials suggested that elements opposed to Afghanistan’s American backed government were stirring the violence, which has also targeted American troops and the United Nations.

The demonstrations could complicate President Karzai’s plans to ask for military aid on a trip to Washington this month, a prospect that has stoked a previously muted debate on how long American troops should stay to secure the country, still riven by a Taliban-led rebellion. That debate may play out in parliamentary elections this year.

The Afghan leader, on a trip to Europe, has played down the violence as the growing pains of Afghan democracy.

The trigger of the unrest was a brief report in the May 9 edition of Newsweek magazine that interrogators at the prison on Guantanamo Bay, Cuba, placed Korans in washrooms to unsettle suspects, and in one case “flushed a holy book down the toilet.”

Desecration of the Koran is punishable by death in both Afghanistan and Pakistan, but diplomats and officials have been taken aback by the intense reaction – further enflamed by bloodshed in a police crackdown on anti-American protesters in the eastern Afghan city of Jalalabad on Wednesday that left four dead and more than 70 wounded.

It was unclear why demonstrations broke out this week and not after previous press reports. In July 2004, for example, the Arab TV station Al-Jazeera ran an interview with a former Guantanamo detainee who claimed he saw an American soldier stomp on the Koran and that another American soldier in the southern city of Kandahar threw a holy book into the toilet.

Pakistan protested to the American government last weekend about the alleged abuse cited in the Newsweek report, giving the article wider play in the region’s press than the Al-Jazeera interview may have received last year.

At the Pentagon, the chairman of the Joint Chiefs of Staff, General Richard Myers, said yesterday that American commanders in Afghanistan believe that local political factions – and not the reports about the alleged desecration – are driving the violence in Jalalabad.

General Myers said the military is investigating the allegation but so far has not been able to confirm it. In one case, an inmate, in an act of defiance, ripped pages out of his Koran and stuffed them into the toilet in an attempt to back up the plumbing, General Myers said, citing logs from the prison.

American officials tried again yesterday to calm tempers, promising a thorough investigation and insisting all inmates at Guantanamo, many of them Pakistanis and Afghans captured after the September 11 attacks, are given Korans, prayer beads, and time to pray.

“Disrespect for the Holy Koran is not now, nor has it ever been, nor will it ever be, tolerated by the United States,” Ms. Rice said in a statement to a Senate appropriations subcommittee.

“Our military authorities are investigating these allegations fully,” she said. “If they are proven true, we will take appropriate action. Respect for the religious freedom for all individuals is one of the founding principles of the United States.”