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The state of emergency, starting at 2 pm GMT on Wednesday, was to last a month.
In the streets around the Rabaa al-Adawiya mosque in northeast Cairo, where thousands of Morsi supporters have staged a sit-in, riot police wearing gas masks crouched behind armoured vehicles, tear gas hung in the air and burning tyres sent plumes of black smoke into the sky.
Cairo Riots (Photo: AP)
The unrest spread beyond the capital, with the Nile Delta cities of Minya and Assiut, and Alexandria on the northern coast, also hit by violence. Nine people were killed in the province of Fayoum south of Cairo. Five more died in Suez.
Seven hours after the initial operation, crowds of protesters were still blocking roads, chanting and waving flags as security forces sought to prevent them from regrouping.
At a morgue near the mosque, a Reuters reporter counted 29 bodies, including that of a 12-year-old boy. Most had died of gunshot wounds to the head. A nurse at the same hospital had said she counted 60 bodies, and expected the number to rise.
"At 7 a.m. they came. Helicopters from the top and bulldozers from below. They smashed through our walls. Police and soldiers, they fired tear gas at children," said teacher Saleh Abdulaziz, 39, clutching a bleeding wound on his head.
"They continued to fire at protesters even when we begged them to stop."
The West, notably the United States which gives the Egyptian military $1.3 billion each year, has been alarmed by the recent violence, and on Wednesday the European Union urged security forces to show "utmost restraint" in a nation that has a peace treaty with Israel and controls the vital Suez Canal waterway.
Military tightens grip
The move to break up the camps appeared to dash any remaining hopes of bringing the Brotherhood back into the political mainstream, and underlined the impression many Egyptians share that the military is tightening its grip.
Dozens wounded in violent protests (Photo: AP)
The operation also suggested the army had lost patience with persistent protests that were crippling parts of the capital and slowing the political process.
It began just after dawn with helicopters hovering over the camps. Gunfire rang out as protesters, among them women and children, fled Rabaa, and smoke rose into the air. Armored vehicles moved in beside bulldozers which began clearing tents.
"Tear gas (canisters) were falling from the sky like rain. There are no ambulances inside. They closed every entrance," said protester Khaled Ahmed, 20, a university student wearing a hard hat with tears streaming down his face.
"There are women and children in there. God help them. This is a siege, a military attack on a civilian protest camp."
A second, smaller camp near Cairo University was swiftly cleared in the early morning.
Nine hours after the start of the operation, crowds of protesters were still blocking roads, chanting and waving flags as security forces sought to prevent them from regrouping.
The government issued a statement saying security forces had showed the "utmost degree of self-restraint", reflected in low casualties compared to the number of people "and the volume of weapons and violence directed against the security forces".
It added that it would press ahead with implementing an army-backed political transition plan in "a way that strives not to exclude any party from participation".
The government, which envisages holding new elections in about six months to return democratic rule to Egypt, urged the protesters not to resist the authorities, adding that Muslim Brotherhood leaders must stop inciting violence.
"The government holds these leaders fully responsible for any spilt blood, and for all the rioting and violence going on," the statement added.
Condemnation, rising concern overseas
Security officials said senior Muslim Brotherhood politician Mohamed El-Beltagi had been arrested during Wednesday's crackdown. A grouping of the movement's allies denied the assertion, but said Beltagi's daughter had been shot dead.
The Interior Ministry issued a statement saying Brotherhood leaders had instructed their followers to attack police stations throughout the country.
Live television footage on several channels appeared to show hooded Brotherhood gunmen brandishing what appeared to be small automatic rifles and firing them in the direction of soldiers.
The latest crackdown came after international efforts failed to mediate an end to the political standoff between Mursi's supporters and the army-backed government which took power after his ouster on July 3.
Iran condemned Wednesday's violence and said it increased the likelihood of civil war in Egypt.
Turkey's Prime Minister Tayyip Erdogan called on the U.N. Security Council and Arab League to take immediate steps to stop a "massacre" in Egypt, and the European Union said reports of protesters being killed were "extremely worrying".
Morsi became Egypt's first freely elected leader in June 2012, but failed to tackle deep economic malaise and worried many Egyptians with apparent efforts to tighten Islamist rule.
Liberals and young Egyptians staged huge rallies demanding that he resign, and the army said it removed him in response to the will of the people.
More than 300 people have already died in political violence since Morsi's overthrow, including dozens of supporters killed by security forces in two separate earlier incidents in Cairo.
The unrest has extended political and economic turmoil since a 2011 uprising that ended 30 years of autocratic rule by US-backed President Hosni Mubarak, and the country is now more deeply divided than any time for many years.
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