Demonstrators furious at the trailer of the film made in the US they say insults the Prophet Muhammad also clashed with police near the US embassy in Cairo.
Reporting from Egypt, Al Jazeera's Rawya Rageh said protesters belonging to ultra-conservative groups in Sinai stormed a camp for the UN multinational peacekeepers in Sheikh Zuwayed town. They brought down the flag and placed a black banner with the words "There's no God but Allah, Muhammad is the Prophet of Allah."
In Gaza, thousands of people rallied at demonstrations in Gaza City and the southern town of Rafah, a day after the ruling Hamas party urged citizens to turn out for protests after Friday prayers.
Protesters waved the flags of the Hamas and Islamic Jihad movements, and set fire to American flags, chanting "Death, death to America, death, death to Israel".
The film was blamed for an attack on the US consulate in Libya's eastern city of Benghazi that killed the US ambassador and three other Americans on Tuesday, the anniversary of the September 11, 2001, al-Qaeda attacks on the United States.
Al Jazeera's Hoda Abdel Hamid, reporting from Benghazi, said: "There is a lot of tension in Benghazi people are confused, they want to protest, but after what took at the US consulate, people are apprehensive, Libyan authorities still believe it was a planned attack at the embassy".
In Nigeria, where radical Islamist sect Boko Haram has killed hundreds this year in an insurgency, troops opened fire in the air outside a mosque to disperse protesters in the city of Jos.
