The US boosted security at its embassies amid fears that more anti-American violence sparked by a film mocking Islam could erupt after Friday's Muslim prayers across the Middle East and North Africa.
Four people died in the Yemeni capital Sanaa on Thursday as police fired live rounds and tear gas to try to disperse an angry crowd of hundreds of protesters trying to storm the US mission.
The protests came as US and Libyan officials probed an attack on the consulate in the eastern Libyan city of Benghazi that killed the ambassador and three other US officials on Tuesday, amid growing speculation it was the work of extremist militants rather than just demonstrators.
Two of the four Americans killed in the assault were former members of the elite Navy SEALs officials identified as Tyrone Woods and Glen Doherty. The harrowing attack also left Ambassador Chris Stevens and Sean Smith, an information management officer, dead.
The US embassy in Cairo was under siege for a fourth day after protests spread to several countries and territories, including Bangladesh, Iran, Iraq, Israel and the Gaza Strip, Jordan, Kuwait, Sudan and Tunisia.
Washington sought to keep a lid on the demonstrations by spelling out that the controversial film that set off the violence was made privately by a small group of individuals with no official backing.
"Let me state very clearly -- and I hope it is obvious -- that the United States government had absolutely nothing to do with this video," Secretary of State Hillary Clinton declared in condemning the "disgusting and reprehensible" video.
As enraged demonstrators again took to the streets, Islamist groups in several countries called for greater protests after Friday prayers, a prospect the White House admitted it feared as the United States tightened security at diplomatic missions around the globe.
"We are watching very closely for developments that could lead to more protests," said White House spokesman Jay Carney.
Egypt's powerful Muslim Brotherhood called for nationwide action following evening prayers.
And in Jordan, Salafist militants have said they plan to demonstrate outside the US embassy in Amman after midday prayers.
Libyan Prime Minister Mustafa Abu Shagur told AFP in an exclusive interview that a "big advance" had been made in the probe into the Benghazi attack following several arrests.
"We have some names and some photographs," he said.
A security official in Yemen said that in addition to those killed in the clashes, another four people had been wounded, eight of them seriously. The unrest lasted from morning until late evening.
Troops deployed on the rooftops of buildings around the US mission in Sanaa and police used water cannon and fired warning shots to drive out protesters who had breached the perimeter wall.
Witnesses said they saw three vehicles being torched by a group of demonstrators that gained access to the compound through an unguarded security gate.
Yemeni President Abdrabuh Mansur Hadi apologised to US President Barack Obama for the acts of a "mob" and ordered an investigation.
Egypt's Islamist President Mohamed Morsi has warned against resorting to violence but his angry statements about the film and failure to immediately apologize over the storming of the US embassy have Washington on edge.
Violence rocked the Egyptian capital, where police fired tear gas to disperse protests outside the embassy by stone- and bottle-throwing demonstrators.
A total of 224 people were injured, the Egyptian health ministry said.
The violence began on Tuesday night, when protesters stormed the Cairo embassy compound, tearing down the Stars and Stripes and replacing it with a black Islamic flag.
Obama acknowledged late Wednesday that ties with the new Egypt were a "work in progress" and seemed to be signal a review of its status, by saying Cairo could neither be considered an ally nor an enemy.
Amid the mounting protests, Russian President Vladimir Putin warned the Middle East "may descend into chaos."
The crisis also reverberated in the US presidential race as Republican challenger Mitt Romney insisted that US power was vital in the region but halted his criticism of Obama's handling of the crisis.
The White House hopeful sparked a furore on Tuesday when he offered a quick and blunt rebuke of the Obama administration's efforts to tamp down the rapidly escalating protests.
The catalyst for the bloody conflagration in the Muslim world was an amateurish film denigrating the Prophet Mohammed and linked to evangelical and Coptic Christians in the United States.
The suspected producer is Nakoula Basseley Nakoula, a 55-year-old Copt living in California. It was promoted on the websites of two other Americans, extremist Christian pastor Terry Jones and another Copt, Washington-based lawyer Morris Sadek.
Both the State Department and the White House say there is nothing they can do to stop individuals producing inflammatory material because of freedom of speech laws enshrined in the First Amendment of the US constitution.
UN leader Ban Ki-moon condemned the "hateful" anti-Islam film as deliberately intended to incite bigotry.