At least 13 people were killed as security forces tried to clear protesters from Cairo's Tahrir Square, casting a dark shadow over Egypt's first elections since Hosni Mubarak's downfall.
Police and military forces used batons, tear gas and birdshot to clear the central square of thousands of protesters demanding that the ruling military cede power to a civilian authority.
It was the second day of violence in the Egyptian capital, following a peaceful anti-military mass rally on Friday.
Morgue officials said 13 people died on Sunday and two people on Saturday, kicking off a violent countdown to the country's first elections since the end of former president Mubarak's 30-year-rule.
The legislative elections are due on November 28.
Early Monday the imam of the Omar Makram mosque on Tahrir Square, Sheikh Mazhar Shahin, told public television that calm had returned on the square after he reached an agreement with the security forces.
Shahin said he had met with a delegation from the army and police to set up a ceasefire.
The morgue officials said that at least four people had been shot dead on Sunday.
The health ministry said 10 were killed Sunday and 1,700 wounded over the weekend in the clashes, in a statement to the official MENA news agency.
Earlier Dr Mohammed Fatuh, who heads a field hospital in the square, confirmed to AFP that three more bodies had been brought in bearing bullet wounds.
Police and troops seized the square -- the symbolic heart of protests that toppled Mubarak in February -- only to be beaten back by protesters who retook it later, as had also happened on Saturday.
An AFP reporter said late on Sunday that on one street protesters were throwing stones and petrol bombs at military armored personnel carriers and riot police.
He said military police had responded with mostly shotgun fire and rubber bullets. When there was steady fire some protesters began to run while others chanted "Hold fast! Hold fast!" and "We won't leave!"
There were heavy clashes on side streets leading to the interior ministry as protesters chanted "The people want to topple the field marshal" -- Hussein Tantawi, Mubarak's long-time defense minister who heads the ruling military.
In the Mediterranean city of Alexandria, a funeral procession for one of the victims degenerated into clashes with the police who fired volleys of tear gas at mourners, MENA reported.
In the canal city of Suez, troops fired live rounds into the air to stop protesters from storming a police station in the city centre.
Protests also broke out in the central cities of Qena and Assiut, a security official said, adding that 55 people had been arrested nationwide.
Egypt's cabinet, which held crisis talks for several hours before moving en masse to the headquarters of the ruling Supreme Council of the Armed Forces (SCAF) for another meeting, said in a statement that parliamentary elections scheduled for November 28 would go ahead.
Throughout the day, sporadic clashes erupted near the interior ministry on the outskirts of Tahrir Square, which was covered by clouds of tear gas and littered with stones and glass.
In makeshift hospitals set up in mosques around the square, demonstrators were treated for tear gas inhalation and injuries from rubber bullets and birdshot.
The SCAF, in a statement read out on state television, said it "regretted" what was happening. It said it was committed to the elections timetable.
Earlier Mohsen al-Fangari, a member of the council, insisted the election would go ahead as planned and that the authorities were able to guarantee security.
"We will not give in to calls to delay the elections. The armed forces and the interior ministry are able to secure the polling stations," Fangari told a talk show on the Egyptian satellite channel Al-Hayat.
Several prominent political figures and intellectuals, including former UN nuclear watchdog chief Mohamed ElBaradei, earlier issued a call for a delay to the legislative polls.
They submitted a new transition roadmap which would see an elected constituent assembly draft a constitution and then a presidential election would be held, followed by parliamentary polls.
The recent street protests have seen the return of riot police, the branch of the interior ministry most used by the Mubarak regime in its crackdown against protesters but rarely deployed since.
Friday's rally, which grouped Islamist and secular activists, called on the military to hand power to a civilian government. It also demanded more control over the constitution the new parliament is to draft.
Protesters called for the withdrawal of a government document that proposes supra-constitutional principles, which could see the military maintain some control over the country's affairs and keep its budget from public scrutiny.
The military says it will hand over power after a presidential election, which has yet to be scheduled.
Friday's demonstration passed without incident, but when demonstrators returned to the square on Saturday, they were met with violence by security forces.
On Saturday, medics announced the deaths of Ahmed Mahmoud, 23, who sustained a bullet wound to the chest in Cairo, and Baha Eddin Mohammed Hussein, 25, hit by a rubber bullet in Alexandria as protests spread.
In Brussels, the European Union called on Egypt to respect human rights.
"I urge calm and restraint and condemn the use of violence in the strongest terms," the EU's foreign policy chief Catherine Ashton said in a statement.
"Law and order must be ensured in a manner respectful of human rights," she added.