In Cairo, several men scaled the walls of the U.S. Embassy and tore down its American flag, according to CNN producer Mohamed Fadel Fahmy, who was on the scene.
The group then clashed with security forces in the city, blocking roads leading to the consulate, witnesses said.
The Libyan government notified the United States that an employee at the U.S. Consulate was killed, a State Department official told CNN.
The State Department does not have independent confirmation of the death, the official said. The nationality of the worker was not immediately known.
Libya's General National Conference condemned the attack, saying it "led to the regrettable injury and death of a number of individuals." Lawmakers said in a statement Tuesday night that they were investigating.
It was unclear whether the two attacks were coordinated, CNN national security contributor Fran Townsend said Tuesday night.
"One such breach of an embassy or consulate's walls or security on any given day would be tremendous news. ... The fact that two of them happened on the same day that is the 9/11 anniversary where Americans are remembering those that we lost, you have to ask yourself, what are American officials trying to understand about this and whether or not these two are related?" she asked.
In Egypt, police and army personnel formed defensive lines around the U.S. Embassy in an effort to prevent demonstrators from advancing, but not before the protesters affixed a black flag atop a ladder in the American compound.
The black flag, which hangs in full view from inside the complex, is adorned with white characters that read, "There is no God but Allah and Mohammed is his messenger," an emblem often used by Islamic radicals.
A volley of warning shots were fired as a large crowd gathered around the compound, although it is not clear who fired the shots.
Egyptian groups point to U.S. websites, including YouTube, that have scenes from the film. Some anti-Muslim blogs also have flagged the movie.
In a series of disjointed scenes, filmmakers depict Prophet Mohammed as a child molester, womanizer and ruthless killer.
Most of the Muslim world considers depictions of Mohammed to be blasphemous and deeply offensive.
It was not clear late Tuesday who produced the film and under what auspices.
Embassy officials issued a warning to Americans in Egypt, telling them to avoid the demonstrations which "may gather in front of the U.S. Embassy, or Egyptian government buildings such as the People's Assembly and Ministry of Interior."
"It is unclear if large numbers will take to the streets, but clashes may occur should two opposing groups come into contact with one another," the U.S. Embassy said in a statement. "Large gatherings and non-essential travel in and around downtown and Garden City should be avoided this afternoon."
Frenzied protesters could been seen Tuesday afternoon holding up bits of a shredded American flag to television camera crews while chanting anti-U.S. slogans.