The crowd grew throughout the evening with thousands standing outside the embassy. Dozens of riot police lined up along the embassy walls but did not stop protesters as they continued to climb and stand on the wall - though it appeared no more went into the compound.
The crowd chanted, "Islamic, Islamic. The right of our prophet will not die." Some shouted, "We are all Osama," referring to al-Qaida leader bin Laden. Young men, some in masks, sprayed graffiti on the walls. Some grumbled that Islamist President Mohammed Morsi had not spoken out about the movie.
A group of women in black veils and robes that left only their eyes exposed chanted, "Worshippers of the Cross, leave the Prophet Muhammad alone."
By midnight, the crowd had dwindled. The U.S. Embassy said on its Twitter account that there will be no visa services on Wednesday because of the protests.
A senior Egyptian security official at the embassy area said authorities allowed the protest because it was "peaceful." When they started climbing the walls, he said he called for more troops, denying that the protesters stormed the embassy. He spoke on condition of anonymity because he was not authorized to speak to reporters.
The Cairo embassy is in a diplomatic area in Garden City, where the British and Italian embassies are located, only a few blocks away from Tahrir Square, the center of last year's uprising that led to the ouster of Hosni Mubarak. The U.S. Embassy is built like a fortress, with a wall several meters (yards) high. But security has been scaled back in recent months, with several roadblocks leading to the facility removed after legal court cases by residents.
The Egyptian Foreign Ministry promised in a statement to provide the necessary security for diplomatic missions and embassies and warned that "such incidents will negatively impact the image of stability in Egypt, which will have consequences on the life of its citizens."
One protester, Hossam Ahmed, said he was among those who entered the embassy compound and replaced the American flag with the black one. He said the group has now removed the black flag from the pole and laid it instead on a ladder on top of the wall.
"This is a very simple reaction to harming our prophet," said another, bearded young protester, Abdel-Hamid Ibrahim.
In Washington, State Department spokeswoman Victoria Nuland said Egyptian police had removed the demonstrators who entered the embassy grounds.
Muslims find it offensive to depict Muhammad in any fashion, much less in an insulting way. The 2005 publication of 12 caricatures of the prophet Muhammad in a Danish newspaper triggered riots in many Muslim countries.
A 14-minute trailer of the movie that sparked the protests, posted on the website YouTube in an original English version and another dubbed into Egyptian Arabic, depicts Muhammad as a fraud, a womanizer and a madman in an overtly ridiculing way, showing him having sex and calling for massacres.
A YouTube spokesperson said the website would not take down the video at this point. The website's guidelines call for removing videos that include a threat of violence, but not those only expressing opinions. YouTube's practice is not to comment on a specific videos.
"We take great care when we enforce our policies and try to allow as much content as possible while ensuring that our Community Guidelines are followed," the YouTube spokesperson said. "Flagged content that does not violate our Guidelines will remain on the site."
Sam Bacile, an American citizen who said he produced, directed and wrote the two-hour film, said he had not anticipated such a furious reaction.
"I feel sorry for the embassy. I am mad," Bacile said.
Speaking from a telephone with a California number, Bacile said he is Jewish and familiar with the region. Bacile said the film was produced in English and he doesn't know who dubbed it in Arabic. The full film has not been shown yet, he said, and he said he has declined distribution offers for now.
"My plan is to make a series of 200 hours" about the same subject, he said.
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