Thousands of Egyptian demonstrators have torn down the Stars and Stripes at the US embassy in Cairo and replaced it with an Islamic flag on the anniversary of the September 11, 2001,  attacks in the US.

Nearly 3,000 demonstrators, most of them Islamist supporters of the Salafist movement or football fans, gathered on Tuesday at the embassy in protest over an amateur film deemed offensive to the Prophet Muhammad which was produced by expatriate members of Egypt's Christian minority resident in the US.

A dozen men scaled the embassy walls and one of them tore down the US flag, replacing it with a black one inscribed with the Muslim profession of faith: "There is no God but God and Mohammed is the prophet of God."

Demonstrators also daubed part of that slogan - "There is no God but God" - on the walls of the embassy compound.

"So far, we haven't had any statements coming from authorities in Egypt," Al Jazeera's Adam Makary reported from Cairo.

He quoted sources as saying that the US embassy was working with Egyptian security forces in trying to calm the situation.

Egyptian police intervened without resort to force and persuaded the trespassers to come down.

The crowd then largely dispersed leaving just a few hundred protesters outside the US mission.

Asked whether the flag the protesters hoisted on the anniversary of the killing of nearly 3,000 people in Washington, New York and Pennsylvania was an al-Qaeda flag, a US state department official said she thought not.

"We had some people breach the wall, take the flag down and replace it. What I heard was that it was replaced with a plain black flag. But I maybe not be correct in that," she said.

Egyptian activist Wael Ghoneim wrote on his Facebook page that "attacking the US embassy on September 11 and raising flags linked to Al-Qaeda will not be understood by the American public as a protest over the film about the prophet.

"Instead, it will be received as a celebration of the crime that took place on September 11," he said.

Americans on Tuesday marked the 11th anniversary of the September 11, attacks in which nearly 3,000 people were killed when hijacked airliners slammed into the Pentagon and New York's World Trade Centre and another was brought down in Pennsylvania.