Soldiers killed at least 10 people in Cairo over the weekend, including two protesters whose beating deaths were filmed by a local television station.
At least 300 people were injured in the clashes as demonstrations resumed in central Tahrir Square after the second round of elections to the lower house of parliament.
The disturbances were not the only problem facing Egypt's military council, which is trying to preserve the country's secular character.
A new civilian advisory council set up to offer policy guidance said it would suspend its meetings until the violence stopped. It wants the people responsible for the violence prosecuted and has asked the army to release all those detained in the unrest. One council member announced he was quitting.
In the first round of elections, Islamist parties won nearly 70 percent of the 150 parliamentary seats up for grabs, with 73 going to the Muslim Brotherhood and 30 to the Salafists. The Islamists seem to headed for certain victory in the second phase as well.
Prime Minister Kamal al-Ganzouri, who was appointed only a few weeks ago in response to the violent clashes in Tahrir Square last month, blamed "foreign elements" for the weekend violence by demonstrators. That cannot be ruled out entirely, but it is difficult to argue with the images showing soldiers beating two demonstrators to death.
The private Egyptian television channel CBC broadcast live footage of soldiers repeatedly beating and kicking two protesters lying on the ground until they stopped moving. Demonstrators later said the two died of their injuries.
Security forces also fired live ammunition at protesters in central Cairo on Thursday in an effort to quell the protests.
Protesters fled into side streets to escape the troops in riot gear, who grabbed people and battered them repeatedly even after they had been beaten to the ground, a Reuters journalist said. Shots were fired in the air.
Soldiers pulled down protester tents and set them on fire, local television footage showed.
In Reuters footage, one soldier in a line of charging troops drew a pistol and fired a shot at retreating protesters. It was not clear whether he was using blanks or live ammunition.
Ganzouri said 30 security guards outside parliament had been hurt.
Tahrir protesters and other Egyptians are infuriated by the army's perceived reluctance to quit power, focusing their wrath on Field Marshal Mohamed Hussein Tantawi, head of the military council, who was for two decades defense minister to deposed President Hosni Mubarak.
The protesters demand the council's immediate dismissal; the council is supposed to hand over power after the presidential election scheduled for June.
The army assault on Thursday that followed skirmishes between protesters and troops during which a fire destroyed archives, some more than 200 years old, in a building next to Tahrir Square.
An army official said troops targeted thugs, not protesters, after shots were fired at soldiers and Molotov cocktails set the archive building ablaze, the state news agency MENA reported.
The French Foreign Ministry said in a statement it was concerned about the violent incidents at Tahrir and condemned the "excessive use of force" against protesters in Cairo.
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