They also issued a statement denouncing the United States and Israel and those who support the film which mocks the Prophet Mohammad.
"This kind of insult has spread through many countries in Europe as well as America. They're trying to destroy our prophet Mohammad's image. We Muslims around the world cannot accept this," said Syed Sulaiman Hussaini, a protest leader.
Traffic on Wireless Road in front of the embassy temporarily closed. Protesters burned the US flag amid heavy rain before they dispersed.