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According to wire reports, a U.S. official said that nearly all the embassy staffers had been sent home before the protest and that the ambassador was out of town. It was not immediately clear whether any staff members had remained inside to watch the events unfold through the building’s windows.

Officials in Washington were somewhat slow to make sense of the protest, news of which broke as the State Department opened its daily news briefing.

“We are obviously working with Egyptian security to try to restore order at the embassy and to work with them to try to get the situation under control,” Mrs. Nuland said.

“Obviously, one of the things about the new Egypt is that protest is possible,” she added. “Obviously, we all want to see peaceful protest, which is not what happened outside the U.S. mission, so we’re trying to restore calm now.”

A statement posted on the website of the U.S. Embassy in Cairo made no reference to the rally or the tearing down of the American flag.

The attacks were believed to be a response to a U.S.-produced film that the attackers believed was blasphemous to Islam.

The U.S. embassy in Cairo had issued a statement during the day that criticized the makers of the film.

“The Embassy of the United States in Cairo condemns the continuing efforts by misguided individuals to hurt the religious feelings of Muslims — as we condemn efforts to offend believers of all religions,” the statement read. “Today, the 11th anniversary of the September 11, 2001, terrorist attacks on the United States, Americans are honoring our patriots and those who serve our nation as the fitting response to the enemies of democracy.

“Respect for religious beliefs is a cornerstone of American democracy,” the statement said. “We firmly reject the actions by those who abuse the universal right of free speech to hurt the religious beliefs of others.”

It’s likely that the storming of the embassy occurred after officials posted the statement, which apparently was meant to calm local anger over the recently produced film critical of the Prophet Muhammad.

Clips of the film, which Egyptian media reports said was produced in the U.S. by an anti-Muslim group, could be viewed Tuesday on YouTube. The film depicts Muhammad as a fraud, showing him having sex and calling for massacres.

Muslims find it offensive to depict Muhammad in any fashion, much less in an insulting way.

The flag flown by the protesters is black and bears in white Arabic lettering the first line of the Muslim creed: “There is no God but Allah, and Muhammad is his prophet.” Beneath the slogan is the seal of Muhammad.

The flag was first used by al Qaeda during its insurgency in Iraq, according to Aaron Y. Zelin, a fellow at the Washington Institute for Near East Policy. But it has since been widely adopted by other Islamist extremists.

“Muhammad flew a white flag in peace and a black one in war,” said Mr. Zelin, adding that the flag’s color makes it in effect a military standard.

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