By nightfall, the military-backed interim government that replaced Morsi after a July 3 coup had declared a state of emergency, and Mohamed ElBaradei, the Nobel Peace Prize winner and vice president, had tendered his resignation in protest over the bloody crackdown.
The United States strongly condemned the violence and said it would hold the interim Egyptian government accountable for its promises of a speedy transition to a democratically elected civilian administration.
Hundreds of Morsi-allied Muslim Brotherhood members were arrested nationwide after the dawn assault, the Egyptian government said. The authorities blamed the Islamist group for the violence and said police had confiscated guns, ammunition and other weapons from the protest sites at Rabaa al-Adawiya and Nahda squares.
The raid brought bulldozers crashing through protesters’ tents as security forces opened fire through clouds of smoke and tear gas. Witnesses later posted footage showing dozens of bodies lining the rooms of a makeshift hospital run by Morsi supporters outside the Rabaa al-Adawiya mosque.
Mohamed el-Beltagi, a top Brotherhood politician whose teenage daughter was among those killed, said security forces had sacrificed their legitimacy by carrying out the attack, and he demanded that any soldier “must take off his uniform’’ or be considered a “tool” of the government. He warned that the spreading violence could quickly turn Egypt into a new Syria, where an ongoing conflict has killed more than 100,000 people.
Egypt’s interim interior minister said Brotherhood supporters later stormed several provincial headquarters across the country and set as many as seven Christian churches ablaze. The sectarian attacks reflect Islamist anger over the strong backing for the military shown by many members of Egypt’s Christian minority.
The sprawling tent cities of men, women and children had been erected by Brotherhood supporters to demand the reinstatement of Morsi, Egypt’s first democratically elected president. On Wednesday evening, the interim prime minister and the interior minister said security forces had acted with the utmost “self-restraint” after six weeks of unauthorized sit-ins by Morsi’s supporters.
The government said 43 police officers were killed in the clashes. In addition to scores of protesters, the dead included at least two journalists, including a British cameraman for Britain’s Sky News network.
The large-scale arrests of Muslim Brotherhood members echoed the authoritarian approach adopted by the government during the Mubarak era, when the Islamist group was banned and heavily repressed. The Brotherhood’s Freedom and Justice Party, which backs Morsi, had emerged after Mubarak’s fall as the country’s strongest political force. But the group’s popularity plummeted under Morsi, as Egyptians complained of a sinking economy and little political reform.
The party said the death toll in the crackdown is far higher than the government acknowledges, putting the number at more than 2,000. The figure could not be verified.
In his letter of resignation, ElBaradei, the vice president, stopped short of criticizing the security forces or military directly. But he said it had “become difficult for me to hold responsibility for decisions that I do not agree with, whose consequences I fear.’’
“I cannot be responsible for one drop of blood in front of God, and then in front of my conscience, especially with my faith that we could have avoided it,” ElBaradei said in the letter to Adly Mansour, the interim president.
Speaking from Martha’s Vineyard, where President Obama is vacationing, deputy press secretary Josh Earnest said “the world is watching” events in Cairo. He said the White House had urged the interim government and all parties in Egypt “to refrain from violence and resolve their differences peacefully.”
The military has held Morsi and his top aides, as well as other prominent Islamist leaders, virtually incommunicado since the coup. Last month, Egyptian prosecutors said they were investigating the former president on charges of murder and treason.
Morsi supporters outside Rabaa al-Adawiya acknowledged Wednesday morning that they had heard the government’s warnings of a raid for weeks. They said black-clad riot police and plainclothes men in flak jackets moved into the camps about 7 a.m., confronting protesters from multiple side streets with a barrage of tear gas and then gunfire.
Local television footage showed protesters streaming out of the Rabaa al-Adawiya sit-in Wednesday evening, some of them running with children, their hands held up in surrender, as security forces pushed further into the camp. Footage posted online also purported to show pro-Morsi demonstrators firing assault rifles.
The attacks set off retaliatory clashes and protest marches. Crowds of Morsi supporters marched toward eastern Cairo in the late morning, running into a barrage of gunfire as they confronted police lines. Others hurled stones and molotov cocktails as they clashed with anti-Islamist civilians elsewhere in the capital and in cities across this vast nation of 85 million.
The state-run Middle East News Agency said Muslim Brotherhood supporters set fire to the government headquarters in the coastal city of Alexandria and attacked government offices in the Nile Delta city of Damanhour. In the southern Islamist stronghold of Beni Suef, Morsi supporters occupied the provincial headquarters and took three soldiers hostage, state media said.
Government officials said Egypt’s stock market and banks were closed and would remain so through Thursday.
On the ground
In Cairo, Islam Fathi, a 20-year-old university student from the Nile Delta town of Mansoura, was among the Morsi supporters who had manned a sandbag perimeter overnight at the Rabaa al-Adawiya site. He said protesters had begun to relax after dawn prayers when the police assault began.
Fathi said he and others fled to a nearby cafe but were confronted by police, who struck them and ordered them toward a van. “They took our money and our phones,” he said. Several of the detainees were released, he said; others were not.
By late morning, tents were torn and strewn about at the site as military helicopters circled overhead. By Wednesday night, TV footage showed fires burning across vast swaths of Cairo’s neighborhoods, where clashes had raged.
“I was here every day. There was no violence inside,” one female bystander said. “I’d come for a few hours, then go home.’’
Not far away stood a line of hulking blue trucks, the kind used to haul prisoners that had been ubiquitous during protests under Mubarak. “Anybody who speaks any small words, they take them in the police vans,” said the woman, who didn’t have a chance to give her name because a sudden barrage of tear gas sent her and other bystanders running for cover.
As noon approached, a protester declared, “We’ve started a new beginning. It was peaceful before. I don’t think it will be peaceful now.”
William Branigin in Washington contributed to this report.