The violence prompted vice president and Nobel laureate Mohamed ElBaradei to resign, saying his conscience was troubled over the loss of life, “particularly as I believe it could have been avoided”.
“It has become too difficult to continue bearing responsibility for decisions I do not agree with and whose consequences I fear,” he said.
The state of emergency went into effect at 4:00 pm (1400 GMT) on Wednesday, with daily overnight curfews from 7:00 pm to 6:00 am.
The dramatic descent on the squares shortly after dawn came as a surprise to many. Security officials had originally spoken of gradually dispersing the sit ins over several days.
Shortly after dawn on Wednesday, witnesses and an AFP correspondent said security forces fired tear gas before surging into Rabaa al-Adawiya, sparking pandemonium among the thousands of protesters who had set up the camp soon after Morsi was ousted in a military coup on July 3.
Men in gas masks rushed to grab each canister and dunk them in containers of water, as the main stage near the mosque of the camp blared Islamic anthems and protesters chanted “Allahu Akbar” (God is greatest).
Many Morsi supporters were given safe passage out of the camp, some flashing victory signs as they left through a security corridor.
A security official told AFP that hundreds of people were taking advantage of the safe passage offer, but that some diehards had stayed behind to fight on.
By Wednesday evening, a security official said Rabaa al-Adawiya was “totally under control”, adding: “There are no more clashes”.
In the smaller of the protest camps, at Al-Nahda square in central Cairo, police said they had control of the area after two hours.
Television footage showed flattened tents, as women and children flanked by police and army troops were led out of the square.
Dozens rounded up in the dispersal were shown sitting on the ground, handcuffed and surrounded by security forces.
Authorities later said calm had been restored across the country.
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