Security forces dragged supporters of deposed president Mohamed Morsi from the Al-Fath mosque, passing through angry crowds who tried to beat the Islamists, calling them “terrorists”.
The clashes came as the government said 173 people had been killed in the past 24 hours alone, bring the country’s death toll to more than 750 since Wednesday, when police cleared two camps of Morsi loyalists in the capital.
According to an AFP tally, at least 1,042 people have been killed since June 26, when Morsi supporters began protesting before mass demonstrations against the Islamist leader that prompted the military to end his single year of turbulent rule on July 3.
International criticism of the bloodshed mounted, with Germany and Qatar jointly condemning “the ongoing and brutal violence”.
The standoff at Al-Fath mosque in central Ramses Square began on Friday, with security forces surrounding the building where Islamists were sheltering and trying to convince them to leave.
An Egyptian boy runs after police exchanged gunfire with Morsi supporters holed up in a Cairo mosque
The Islamists had lined up the bodies of dozens of protesters who had been killed on Friday inside the mosque-turned-morgue.
By Saturday afternoon, the situation turned violent, with an AFP reporter on the scene saying gunmen inside the mosque were trading fire with police outside.
Police eventually dragged people from inside the mosque, firing in the air to hold back residents of the area who tried to attack the Islamists with sticks and iron bars.
Both outside the mosque and in several other parts of Cairo, residents targeted those suspected of being Islamists, often for no more than wearing a beard or a veil.
On Friday, Morsi supporters had announced “Friday of anger” demonstrations, which quickly turned violent, with gunshots ringing out in Cairo.
The government said those clashes killed least 173 people across the country, including 95 in the capital and 25 in Alexandria.
Among those killed on Friday was a son of Mohamed Badie, chief of Morsi’s Muslim Brotherhood movement.
It was not clear whether that call had been heeded, with no reports of demonstrations in Cairo on Saturday.
The interior ministry said it had arrested 1,004 Brotherhood “elements”, and on Saturday security sources said the brother of Al-Qaeda chief Ayman al-Zawahiri had been detained.
Security sources also said one soldier was killed in northern Sinai where militants have launched daily attacks against security forces.
Egypt’s interim army-backed government has defended its actions, with presidential adviser Mustafa Hegazy saying the country’s forces had acted with “a huge amount of self-restraint and self-control”.
The cabinet has also insisted the security services were acting to confront a “terrorist plot”.
But international criticism continued to pour in on Saturday, with Germany’s foreign minister and his Qatari counterpart condemning the spiralling violence after a meeting.
“We are deeply distressed by the ongoing and brutal violence in Egypt,” German Foreign Minister Guido Westerwelle said, urging dialogue.
“Otherwise there is great danger that more blood will spill… which indicates the danger of civil war,” he said.
EU leaders have pledged a strong response to the violence, which EU foreign policy chief Catherine Ashton has described as “shocking”.
In Turkey, which backs Morsi, thousands marched in Istanbul against his ouster, and the Vatican said Pope Francis was following events with “mounting concern”.
He was praying for the rival sides to “choose the path of dialogue and reconciliation,” the Vatican said.
The United States has announced the cancellation of its biannual military exercise with Egypt, but stopped short of suspending $1.3 billion in annual aid.
On Saturday, the US embassy said it would not open its doors on Sunday, a working day in Egypt, saying the “possibility of protests in vicinity of the embassy continues”.
Anti-American sentiment has risen in Egypt with Washington’s criticism of the crackdown.
But the international response has been not uniformly critical. Saudi Arabia and Jordan said they backed Egypt’s fight against “terrorism”.
In neighbouring Libya, meanwhile, an explosive device went off in front of the Egyptian consulate in the eastern city of Benghazi, causing damage but no casualties, a security official said.
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