The interior ministry issued a statement saying security forces were taking "necessary measures" against the protesters, who want Morsi reinstated, at the Rabaa al-Adawiya mosque in the east of Cairo and the protest in Nahda Square.
According to the ministry 200 people have been arrested, including 50 in the Rabaa al-Adawiya sit-in in Nasr City and 150 at the Nahda Square sit-in in Giza.
Bulldozers were said to have been used to uproot the camps that had been in place after 62-year-old Morsi was ousted by the military on July 3.
Al Jazeera quoting sources on the ground reported at least 40 fatalities, while the Muslim Brotherhood said at least 300 people had been killed, with more than 5,000 others injured.
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However, the Health Ministry said at least nine people had been killed, including three members of the security forces, and 78 injured.
The statement from the Interior Ministry said a safe exit would be provided for protesters and they would not be pursued, "except those who are wanted by the prosecution".
The interior ministry is keen "not to shed any Egyptian blood", the statement said.
Large plumes of smoke rose over parts of the city as the operation to clear the camps continued.
At least one member of the security forces is among the dead, media reports said.
In response to the security operation, the Muslim Brotherhood urged Egyptians to take to the streets to "stop a massacre".