US officials were, however, were reluctant to establish any link between the two incidents on Tuesday in Cairo, the Egyptian capital, and Benghazi, the Libyan city.
"We cannot confirm any connection between these incidents," a senior State Department official said in response to questions linking the two incidents.
'Anti-Islam' film: US government buildings attacked in Egypt, Libya; one official dead
Multiple American media outlets said that one US official had been killed in the attack on the American consulate in Benghazi, which was set on fire by militant groups. This was notified to the US by the Libyan Government, CNN reported. But there was no independent confirmation of this by US officials.
However, the State Department confirmed the attack. "We can confirm that our office in Benghazi, Libya has been attacked by a group of militants," the State Department spokesperson, Victoria Nuland, said.
"We are working with the Libyans now to secure the compound. We condemn in strongest terms this attack on our diplomatic mission," Nuland said.
Members of a radical Islamist group had been protesting at the consulate, CNN reported. The protest in Libya was against a film produced in the US, which was also the cause of angry protestors storming the American Embassy in Cairo, who then tore down the American flag and replaced it with a black one.
"The black flag, which hangs atop a ladder inside the compound, is adorned with white characters that read, "There is no God but Allah and Mohammad is his messenger," an emblem often used in al Qaeda propaganda," CNN reported.
The State Department later said that the demonstrators now have been removed from the Embassy compound.
"In Cairo, we can confirm that Egyptian police have now removed the demonstrators who had entered our Embassy grounds earlier today," Nuland said.
CNN reported from Egypt that several individuals claimed responsibility for organising the demonstrations, including Salafist leader Wesam Abdel-Wareth, who is president of Egypt's conservative Hekma television channel.
Mohammed al-Zawahiri -- the brother of al Qaeda's leader Ayman al-Zawahiri -- said that "we called for the peaceful protest joined by different Islamic factions including the Islamic Jihad, Hazem Abu Ismael movement," the news channel said.
Sam Bacile, an American citizen who said he produced, directed and wrote the two-hour film, said he had not anticipated such a furious reaction, Fox news reported. He said the film was produced in English and he doesn't know who dubbed it in Arabic.
"The main problem is I am the first one to put on screen someone who is (portraying) Muhammad. It makes them mad," he said in an interview. "But we have to open the door. After 9/11 everybody should be in front of the judge, even Jesus, even Muhammad," Bacile was quoted as saying.
According to Fox News, Bacile addresses the persecution of Copts in Egypt and blames the US and its allies for fighting Muslims. "The US should fight the ideology, not the people," he said.
Meanwhile, a prominent national Muslim civil rights and advocacy organization called on Muslims in the Middle East to ignore the distribution of a "trashy" anti-Islam film, clips of which are circulating online, that resulted in the attack on the American embassy in Cairo.
"We urge that this ignorant attempt to provoke the religious feelings of Muslims in the Arabic-speaking world be ignored and that its extremist producers not be given the cheap publicity they so desperately seek," said Nihad Awad, national executive director of the Washington-based Council on American-Islamic Relations (CAIR).
"Those who created this trashy film do not represent the people of America or the Christian faith. The only proper response to intentional provocations such as this film is to redouble efforts to promote mutual understanding between faiths and to marginalize extremists of all stripes," he said.
"We condemn the attack on the American embassy, which had nothing to do with the production of this intentionally inflammatory film," Awad said.
Earlier in the day, Nuland said one of the things about the new Egypt is that protest is possible.
"Obviously we all want to see peaceful protest, which is not what happened outside the US mission, so we're trying to restore calm now. But I think the bigger picture is one of the United States supporting Egypt's democratic transition and the Egyptian government very much welcoming and working with us on the support that we have to offer," she told reporters at her daily news conference.