The protesters, many in their teens and moving around in small clusters, pelted police with stones who responded by firing tear gas.
Roads leading up to the embassy in central Cairo were littered with stones and rocks.
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Protesters shuttle between the streets surrounding the embassy and Tahrir Square, the epicentre of Cairo protests.
The Muslim Brotherhood, the country's largest political group and on whose ticket President Mohamed Morsi ran, has called for "peaceful protests" outside mosques across the country after the noon prayer.
Several thousand angry protesters had gathered outside the US embassy on Tuesday. One group breached the wall and brought down the flag.
On Thursday, clashes left 224 people injured, eight of whom were admitted to hospital, said health ministry official Ahmed al-Ansari.
The low-budget movie, in which actors have strong American accents, portrays Muslims as immoral and gratuitously violent.
It pokes fun at the Prophet Mohammed and touches on themes of paedophilia and homosexuality, while showing him sleeping with women, talking about killing children and referring to a donkey as "the first Muslim animal."
