Three senior advisers to Mr. Mubarak’s successor, Mohamed Morsi, resigned during the clashes, blaming him for the bloodshed, and his prime minister implored both sides to pull back in order to make room for “dialogue.”
The scale of the clashes, in an affluent neighborhood just outside Mr. Morsi’s office in the presidential palace, raised the first doubts about Mr. Morsi’s attempt to hold a referendum on Dec. 15 to approve a draft constitution approved by his Islamist allies over the objections of his secular opposition and the Coptic Christian Church.
Periodic gunshots could be heard at the front lines of the fight, and secular protesters displayed birdshot wounds and pellets. But it could not be determined whether the riot police or Islamists or the opposition had fired the guns.
Many in both camps brandished makeshift clubs, and on the secular side a few carried knives. By 3:30 a.m. Thursday, at least four people had died, according to the Ministry of Health, and more than 350 were injured in the fighting. Each side claimed that one of its own had been killed, spurring the fighting.
Thousands joined the battle on each side. The riot police initially tried to fight off or break up the crowds with tear gas, but by about 9:30 p.m. Wednesday, the security forces had all but withdrawn. They continued to try to separate the two sides across one boulevard but stayed out of the battle that raged on all around.
In a city square on the Islamist side of the battle lines, a loudspeaker on the top of a moving car blared out exhortations that the fight was about more than politics or Mr. Morsi.
“This is not a fight for an individual, this is not a fight for President Morsi,” the speaker declared. “We are fighting for God’s law, against the secularists and liberals.”
Protesters reportedly set fire to Muslim Brotherhood political offices in the cities of Suez and Ismailia.
Even after two years of periodic battles between protesters and police, Egyptians said they were shocked and alarmed by the spectacle of fellow citizens drawing blood over matters of ideology or political power.
“It is Egyptian fighting Egyptian,” said Mohamed Abu Shukka, 23, who was blocked from entering his apartment building and shaking his head.
Distrust and animosity between Islamists and their secular opponents have mired the outcome of Egypt’s promised transition to democracy in debates about the legitimacy of the new government and its new leaders’ commitment to the rule of law.
The clashes followed two weeks of sporadic violence around the country since Mr. Morsi, a former leader of the Muslim Brotherhood movement, seized temporary powers beyond the review of any court, removing the last check on his authority until ratification of the new constitution.
Mr. Morsi has said he needed the expanded powers to block a conspiracy by corrupt businessmen, Mubarak-appointed judges and opposition leaders to thwart Egypt’s transition to a constitutional democracy. Some opponents, Mr. Morsi’s advisers say, would sacrifice democracy to stop the Islamists from winning elections.
Mr. Morsi’s secular critics have accused Mr. Morsi and the Islamists of seeking to establish a new dictatorship, in part by ramming through a rushed constitution that they charge could ultimately give new power over society to Muslim scholars and Islamists groups. And each side’s actions have confirmed the other’s fears.
As Wednesday’s clashes began, Vice President Mahmoud Mekke offered a compromise that seemed to go nowhere. Mr. Mekke proposed that both sides agree in advance on a package of amendments to the text of the draft constitution to build more support for it before the Dec. 15 vote.
“All the political forces objecting to some articles in the constitution are welcome to provide suggestions or concepts about the articles,” he said, suggesting that through “calm dialogue” both sides could agree on revisions that would be approved by the future Parliament after ratification.
The vice president, however, did not suggest any means to overcome the lack of trust in the Islamist leaders among the secular opposition, or how to persuade liberals to back down from their vow not to negotiate until Mr. Morsi relinquishes the temporary expansion of his powers and cancels the referendum.
Mohamed ElBaradei, the former United Nations diplomat, was chosen Wednesday as coordinator for the newly unified secular opposition. He urged Mr. Morsi and his allies to “see what is happening in the Egyptian street, the division, the polarization. This is something that leads us to violence and worse.”
“The ball is in his court,” Mr. Mr. ElBaradei said at a news conference in which he threatened a general strike or other action to try to stop the referendum. “Bullying will not yield any results for this country.”
“The people of Egypt will be gathering everywhere,” he added. “We will not finish this battle for our freedom and dignity until we are victorious.”
Mr. Morsi did not respond to the clashes. His party, founded by the Muslim Brotherhood, said it held Mr. ElBaradei and other secular leaders responsible for any violence.
The Brotherhood issued its own statement defending the need for Mr. Morsi’s actions to fight off “treacherous plots” against Egypt’s nascent democracy.
“We are confident that the Egyptian people who made this great revolution that impressed the whole world will not abandon democracy or their revolution,” the group said, “and must support the president they chose freely for the first time in history.”
The Islamists also struck the first blow on Wednesday, in retaliation for a secular demonstration the previous night. Tens of thousands of secular protesters had marched on the presidential palace Tuesday night, and perhaps 100 had set up tents to begin a sit-in just outside the palace walls. Though mostly peaceful, there were isolated episodes of violence, including the looting of a guard house, and protesters had written graffiti insulting Mr. Morsi on the palace walls.
In response, a new Islamist coalition, including the Muslim Brotherhood and several ultraconservative groups, issued a statement denouncing the protesters’ “disgusting practices,” and accusing them of “violence or sabotage.” The groups warned that “the alert masses of the Egyptian people are capable of defending legitimacy and defending the gains of their glorious revolution.” They called their own demonstration for Wednesday afternoon outside of the palace.
When thousands of Islamists began arriving at the tent camp around 4 p.m., a tense standoff quickly turned into a rout as they chased the secular protesters, tearing down their tents and beating those who resisted, according to witnesses and videos. “They came from all sides and they punished us,” said Mohamed Ismail, 28, a coffee shop clerk who was among the protesters. “I got slapped on the face and the back of my head.”
Mohamed Ali, 34, a carpenter and one of the Islamists who uprooted the tents, claimed they had found alcohol, marijuana and treats like apples and other fruit inside. He said they had come to defend democracy and Mr. Morsi’s authority. “He should be supported by anyone who supports democracy,” Mr. Ali said.
A few hours later, large groups of secular protesters began to arrive, and Mr. Ali said they had pelted the Islamists with rocks and empty water bottles. “We acted in self-defense,” he said.
It was uncertain how many of the Islamists belonged to the Muslim Brotherhood and how many to other, more hard-line groups, or to no group at all.
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The New York Times