The health ministry said 13 people were injured during sporadic clashes through the night outside the embassy, where on Tuesday thousands of protesters tore down the Stars and Stripes and replaced it with a black Islamic flag.
The interior ministry said Thursday's clashes were sparked by protesters "who threw stones and bottles at security force members protecting the embassy."
Egypt's government on Wednesday called for restraint while denouncing the film, which also sparked fury in Libya where four Americans including the ambassador were killed when a mob attacked the US consulate in Benghazi.
"The film is offensive to the Prophet and immoral," the cabinet said in a statement read by Prime Minister Hisham Qandil at a news conference.
"We call on the great people of Egypt to exercise restraint when expressing their anger," it said.
Protests against the film were also held on Wednesday outside US missions in Morocco, Sudan and Tunisia. In Tunis, police fired tear gas to disperse a crowd of several hundred.
The low-budget movie, "Innocence of Muslims" 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."
Mystery has deepened over the film, with conflicting accounts from backers and promoters but no one owning up to having actually directed it.
US media initially cited someone claiming to be an American-Israeli calling himself Sam Bacile as saying he made the film on a $5 million budget with the help of 100 Jews, but no record of such a person has been found.
Coptic Christians have been accused of promoting an Arabic-adapted version of the English-language film in Egypt, where clips were shown on an Egyptian television station at the weekend, apparently setting off the protests.