In a troubling indication of the increasingly sectarian nature of Egypt's divisions, Reuters cited state media and security sources as saying that a number of churches had been attacked across Egypt.
Churches were attacked in the Nile Valley towns of Minya, Sohag and Assiut, where Christians escaped across the roof into a neighboring building after a mob surrounded and hurled bricks at their place of worship, state news agency MENA said.
Authorities referred 84 people from the city of Suez, including Muslim Brotherhood members and supporters, to military prosecutors on Thursday on charges of murder and burning churches, the state news agency reported.
As Egypt awoke to the first full day of its month-long state of emergency, Cairo appeared calm.
Traffic flowed through the former site of the Rabaa camp, and many Egyptians expressed support for the army in removing the protest camps. Passing drivers were beeping their horns, shouting "Long live Egypt" and slowing to shake hands with soldiers guarding the scorched area.
"I support the army," said Mohamed, a student. "Now we are free, finally."
A woman called Isra said: "What happened [on July 3] is not a coup, it is a people's revolution. I support anyone who supported us to get rid of the terrorism we saw in the streets in the past year."
But while the streets were quiet, activists rallied online—using social media to collate pictures and first-hand accounts of Wednesday's violence at the Rabaa and Nahda camps.
(Read more: Clashes in Egypt, but investors remain upbeat)
Images of bodies piled high in mosques and other makeshift morgues were posted on Twitter, while on Facebook one activist set up a gruesome gallery showing victims of the violence.
Egypt's Interior Ministry also posted pictures—of the 13 policemen killed by pro-Morsi protesters who fought back during the camp clearances.
El-Haddad said the Muslim Brotherhood and its allies had suffered a "very strong blow" in Wednesday's crackdown, and that the whereabouts of all its key leaders could not be ascertained.
The turmoil is the latest chapter in a bitter standoff between Morsi's supporters and the interim leadership that seized control of the Arab world's most populous country on July 3.
Morsi's removal came after millions of Egyptians massed in the streets at the end of June to call for him to step down, accusing him of giving the Brotherhood undue influence and failing to implement vital reforms or bolster the ailing economy.
Morsi himself has been held at an undisclosed location, and faces charges—brought by the security forces—that he colluded with Palestinian militants.
His detention was extended Thursday for another 30 days.
—By NBC News' Ayman Mohyeldin and Alastair Jamieson. NBC News' Charlene Gubash and Reuters contributed to this report.