The film, "Muhammad's Trial," was produced by Coptic-Christians based in the United States, Ahram Online reported.
Protesters climbed atop the embassy walls and got into the embassy's garden, the report said, where they removed a U.S. flag and replaced it with one bearing the Islamic declaration of faith: "There is no God but Allah and Muhammad is the Prophet of Allah."
Earlier, the U.S. Embassy in Cairo, marking the anniversary of the Sept. 11 terror attacks, said it condemns efforts to offend Muslims.
"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 embassy said in a statement." The 11th anniversary of the Sept. 11, 2001, terrorist attacks on the United States finds "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. We firmly reject the actions by those who abuse the universal right of free speech to hurt the religious beliefs of others."
The statement said several groups were calling for demonstrations in Cairo to protests a range of issues, and "U.S. citizens should avoid areas where large gatherings may occur."