KABUL—The top U.S. commander in Afghanistan said the planned burning of Qurans on Sept. 11 by a small Florida church could put the lives of American troops in danger and damage the war effort.

Gen. David Petraeus said the Taliban would exploit the demonstration for propaganda purposes, drumming up anger toward the U.S. and making it harder for allied troops to carry out their mission of protecting Afghan civilians.

Protesters stage an anti-U.S. rally in Kabul after an American church says it will burn the Holy Koran on the September 11 anniversary. Video courtesy of Reuters.

"It could endanger troops and it could endanger the overall effort," Gen. Petraeus said in an interview. "It is precisely the kind of action the Taliban uses and could cause significant problems. Not just here, but everywhere in the world we are engaged with the Islamic community."

Hundreds of Afghans attended a demonstration in Kabul on Monday to protest the plans of Florida pastor Terry Jones, who has said he will burn copies of Islam's holy book to mark the Sept. 11 terrorist attacks. Afghan protesters chanted "death to America," and speakers called on the U.S. to withdraw its troops. Some protesters threw rocks at a passing military convoy.

Gen. David Petraeus said the planned burning of Qurans on Sept. 11 by a Florida church could put the lives of American troops in danger. AFP/Getty Images

Military officials fear the protests will likely spread to other Afghan cities, especially if the event is broadcast or ends up on Internet video.

Mr. Jones, head of the 50-member Dove World Outreach Center in Gainesville, Fla., said in a statement that "We understand the General's concerns. We are sure that his concerns are legitimate." Nonetheless, he added, "We must send a clear message to the radical element of Islam. We will no longer be controlled and dominated by their fears and threats."

Mr. Jones has been denied a permit for the demonstration, but has said he plans to go forward with the protest.

Rev. Stephanie Sapp, spokeswoman for the center, said no one from the Pentagon or other federal agencies had expressed concern or asked that the event be canceled. She did say that the Federal Bureau of Investigation had discussed security measures.

Pentagon officials said they were not aware that any Defense officials have reached out directly to Mr. Jones. But military officers said they hoped that Gen. Petraeus's statement—an unusual move since military commanders rarely get involved in politics—would convince Mr. Jones to change his plans.

Gen. Petraeus declined to elaborate on the nature of the threats or violence that could occur, but westerners in Afghanistan have been warned away from restaurants and other public places amid the rising tensions.

Other senior military leaders echoed Gen. Petraeus commentsMonday. Lt. Gen. William Caldwell, who oversees the effort to train Afghan security forces said he was informed of the planned Florida protests several days ago by a senior minister in the Afghan government.

Gen. Caldwell said many Afghans do not understand either the U.S. Constitution's First Amendment or the fact that President Barack Obama can't simply issue a decree to stop Mr. Jones from his demonstration. Military officials said they were not trying to deny Mr. Jones his right to free speech, but feared he was not thinking about the consequences of his actions.

"There is no question about First Amendment rights; that is not the issue," Gen. Caldwell said. "The question is: What is the implication over here? It is going to jeopardize the men and women serving in Afghanistan."

Pastor Terry Jones, of the Dove World Outreach Center in Gainesville, Fla., says he will burn copies of the Quran Zuma Press

Military officials also fear that if video of the Quran burning is broadcast in Afghanistan, tensions could rise between NATO forces and the Afghan military and police. Allegations of mishandling the Quran have interrupted Afghan security training at least twice this year, Gen. Caldwell said.

In one instance, a Quran fell to the ground when an American officer opened a locker during an inspection of Afghan trainees' barracks. The rumor quickly spread that the officer had thrown it to the ground, angering the trainees at the camp. "He quickly apologized, but rumors took off like wildfire," Gen. Caldwell said. "It was so hard to get the misperception turned around we stopped all training for the rest of the day."

Reports about the Quran have set off violent protests before. A report in Newsweek, later retracted, that a U.S. interrogator at the Guantanamo Bay prison had flushed a Quran down a toilet set off riots in Afghanistan and elsewhere.

—Gary Fields in Washington contributed to this article.