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CAIRO — Soldiers fired on a Cairo mosque Saturday where supporters of the ousted president, Mohammed Morsi, were sheltering, briefly turning a central thoroughfare into a war zone in a further sign that Egypt’s new military rulers are struggling to impose order days after security forces killed hundreds of anti-government Islamists.

Soldiers and policemen eventually stormed and cleared the Al-Fath Mosque, according to the state news agency. As curfew fell, the details of how the siege ended and how many people might have been injured remained unclear, though there were no reports of large-scale deaths. A witness said dozens of people who had been inside were detained and placed in police trucks and army vehicles.

Egyptian state television declared that “the crisis is over.”

But Sunday brought demonstrations and clashes in several other cities across the country. And the eerie silence from the mosque as the evening curfew took effect signaled only that the military-led government remained determined to crush Egypt’s pro-Morsi protest movement.

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The Muslim Brotherhood, which backs Morsi, and the Brotherhood-led Anti-Coup Alliance called for more protests — every day for the coming week — in the same central square where hundreds of pro-Morsi protesters were killed Friday. But the country’s military-backed government signaled it is not backing down, either.

“This state and this people are now under attack,” said Mustafa Hegazy, an adviser to interim President Adly Mansour. Hegazy said the state would defeat the “terrorists” and would soon implement the political road map laid out by Egypt’s military after it wrested control from Morsi last month.

Arrested Saturday in connection with the raid on the mosque was the brother of al-Qaida chief Ayman al-Zawahri. Officials said he planned to bring in armed groups to provide support to those holed up inside the mosque. Mohammed al-Zawahri, a Morsi ally, is the leader of the ultraconservative Jihadi Salafi group that espouses al-Qaida’s hard-line ideology. He was detained at a checkpoint in Giza, the city across the Nile from Cairo, said an official who spoke on condition of anonymity.

The violence at the mosque came a day after battles throughout Egypt — between security forces and Islamists, and among civilians fighting one another — left at least 173 people dead, according to an official count. That raised the death toll to at least 1,000 since Wednesday, the day security forces ended Islamist sit-ins designed to protest the military’s deposing of the democratically elected president.

The mosque standoff began Friday, when Morsi’s supporters turned the mosque into a field hospital and a morgue during clashes with the security services. It appeared that the security forces this time had worked to try to negotiate an end to the standoff.

But ending the siege was complicated by hundreds of civilian opponents of the Islamists who surrounded the mosque and beat Morsi’s supporters as they emerged, despite attempts by the soldiers to bring out at least some of the Islamists safely. The civilians, armed with rubber hoses, metal pipes or wooden clubs, also attacked or detained journalists in the area.

It was not clear whether the vigilantes surrounding the mosque Saturday had been collaborating with the security services, who have long relied on plainclothes enforcers to brutally break up demonstrations. Some echoed the relentless campaign by government officials and the state news media to paint Morsi’s supporters as terrorists.

Civilian vigilantes have added a layer of menace to Egypt’s violence in recent days, as so-called popular committees set up checkpoints in neighborhoods, searching cars and occasionally robbing their drivers. On Friday, armed men roamed Cairo freely, their allegiances, to Morsi or to the military, unclear.

Standing among the police officers Saturday, a man tried to stir up a crowd. “The mosque is full of weapons,” he said, though a reporter who visited the mosque late Friday saw no weapons inside.

Several reporters were attacked by civilians outside the mosque Saturday, including a reporter for the British newspaper The Guardian, Patrick Kingsley, who wrote on Twitter that he had been surrounded by a mob that “duffed me up a bit,” and that his laptop computer and cellphone had been stolen before he was taken to a police station.

Hegazy, for his part, lashed out at the foreign news media and Western countries for ignoring violence by the Islamists, warning “those who give international, financial or moral cover for the acts of violence and terrorism.”

The standoff at the mosque was emblematic of Egypt’s wider chaos, with no end in sight to a feud between Morsi’s supporters and the military that has devolved into violent conflict since last week.

And, perhaps adding further energy to the cycle of bloodshed and revenge, it was announced that among those who died Friday was Ammar Badie, a son of the Brotherhood’s spiritual leader Mohammed Badie.

Prime Minister Hazem el-Beblawi, who leads the military-backed government, later said authorities had no choice but to use force in the wake of recent violence.

“I feel sorry for valuable blood shed,” el-Beblawi said. However, he cautioned that there will be no “reconciliation with those whose hands are stained with blood or those who hold weapons against the country’s institutions.”

Morsi has been held incommunicado since his ouster. Top Brotherhood leaders including General Guide Deputy Khairat el-Shater were detained last month.

The Egyptian government, meanwhile, said it had begun deliberations on whether to ban the Brotherhood, a long-outlawed organization that swept to power in the country’s first democratic elections a year ago.

Such a ban — which authorities say is rooted in the group’s use of violence — would be a repeat to the decades-long power struggle between the state and the Brotherhood.

For more than a month since the July 3 military overthrow of Morsi, Brotherhood members and supporters have attacked and torched scores of police stations and churches, in retaliation. Shops and houses of Christians have also been targeted.

Such attacks spurred widespread public anger against the Brotherhood, giving the military-backed government popular backing to step up its campaign against the Islamist group.

The unrest in Egypt has raised international concerns over the country’s stability and prompted U.N. Secretary-General Ban Ki-moon to condemn on Saturday both “violent protests” in reference to Brotherhood’s rallies and the authorities’ “excessive use of force.”

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