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Supporters of Morsi, however, said the security forces fired on hundreds of protesters, including women and children, at the sit-in encampment as they performed early morning prayers.
"They opened fire with live ammunition and lobbed tear gas," said Al-Shaimaa Younes, who was at the sit-in. "There was panic and people started running. I saw people fall."
A Muslim Brotherhood spokesman, Mourad Ali, denied any Morsi supporters fired first andsaid the military had warned protesters it will break up the sit-in.
Abu Ubaida Mahmoud, a religion student from Al-Azhar University, said he had been praying when the sit-in’s security teams began banging on metal barricades in warning. He then saw troops coming out of the Guard complex.
"The number of troops that came from inside was stunning," said Mahmoud, who was wounded in the hand. The troops opened fire and "I saw injuries in the chest, the neck, the head and the arm," he said.
A guard at a nearby bank said security forces first moved in on the encampment firing tear gas, then he heard gunfire, though who couldn’t tell who was firing. He said that over recent days the Morsi protesters had imposed their control on the surrounding district and were clearly armed.
At field hospitals set up Morsi supporters, at least six dead bodies were shown laid out on the ground, some with severe wounds, in video aired by Al-Jazeera TV. The bodies had been draped with an Egyptian flag and pictures of Morsi. Pools of blood covered the floor and doctors struggled to deal with gaping wounds among some of the hundreds injured.
Health Ministry spokesman Khaled el-Khatib said initial reports indicated at least 42 fatalities and 322 people wounded. One police officer was also killed, the military’s spokesman said.
Egyptian state TV showed images provided by the military of the scene of the sit-in amid the melee. Dozens of protesters were shown pelting troops with rocks and setting tires on fire. Soldiers in riot gear and carrying shields formed lines a few meters (yards) away.
A fire raged from an apartment in a building overlooking the clashes. Images showed men throwing spears from atop nearby building rooftops. Other protesters were lobbing fire bombs at the troops. It was not clear at what stage in the melee the footage was filmed. Security officers were showing cameras bullet casings, and troops were carrying injured colleagues.
By the afternoon, troops moved in and cleared the sit-in site and blockades on the road. The site of the early morning clashes, a strip of road about a kilometer long (about half a mile), was covered with rocks, shattered glass, shoes, clothes, prayer rugs and personal photographs. A big Morsi banner remained hoisted in front of the Republican Guards’ building. On the ground below it, graffiti read: "Where are our votes?"
Interim President Adly Mansour called for restraint and ordered a judicial inquiry into the killings. Significantly, the statement from his office echoed the military’s version of events, noting that the killings followed an attempt to storm the Republican Guard’s headquarters.
Prosecutors in Cairo also ordered the closure of the Brotherhood party’s headquarters amid investigations into a cache of weapons found there, according to the official Middle East News Agency.
El-Tayeb, the sheik of Al-Azhar also called for an independent investigation into the shooting and for the release of all those detained in recent days, referring to five Brotherhood leaders detained since Morsi’s fall.
Morsi supporters have been holding rallies and a sit-in outside the Republican Guard building and elsewhere around Cairo since the military deposed Morsi on Wednesday. The military chief replaced Morsi with an interim president until presidential elections are held. The transition plan is backed by liberal and secular opponents of Morsi, and had been also supported by the ultraconservative Islamist Al-Nour party and both Muslim and Christian religious leaders.
Al-Nour party spokesman Nader Bakkar said on his Twitter account his party is withdrawing its support for the transition plan in response to the "massacre."
Morsi’s supporters refuse to recognize the change in leadership and insist Morsi be reinstated, and have vowed to continue their sit-ins outside the Republican Guard building as well as at a nearby mosque.
Morsi’s opponents are also holding rival rallies. They say the former president lost his legitimacy by mismanaging the country and not ruling democratically, leading to a mass revolt that began June 30, the first anniversary of Morsi’s assumption of power.
Associated Press correspondent Paul Schemm contributed to this report.
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