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.
Conflicting reports emerged over the number of people killed today.
Al Jazeera news channel reported that 94 people were killed, even as Morsi's Muslim Brotherhood claimed the death toll was as high as 2,200, with about 10,000 injured.
According to the Interior 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.
Also Read
Live footage from Cairo this morning showed smoke engulfing Nahda Square, which was later completely cleared, and there were reports of tear gas and birdshot being used on supporters of Morsi.
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.
Witnesses said that after firing tear gas into the Rabaa al-Adawiyeh sit-in, pandemonium struck among the thousands of protesters.
Two journalists were also killed while covering the violence today. Mick Deane, a cameraman for the UK-based Sky News channel, and Habiba Abd Elaziz, a reporter for the UAE-based Xpress newspaper, died from gunshot wounds.
Protesters have camped in Cairo demanding the reinstatement of Morsi, who was country's first democratically elected president and his Freedom and Justice Party was the largest political group in the now dissolved parliament.