The nationwide state of emergency will be in force from 4:00 pm (local time), the presidency said in a statement read out on state television.
The emergency will be in place for one month. The state of emergency enables the army to take all necessary measures to impose and retrieve security.
The interior ministry issued a statement earlier 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. Security forces said 95 people have been killed and 758 injured. However, 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.
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.
In a press conference, the cabinet media adviser thanked the security forces for "exercising self-control and high-level professionalism in dispersing the sit-ins," and held the Muslim Brotherhood responsible for "escalation and violence".
Witnesses said that after firing tear gas into the Rabaa al-Adawiyeh sit-in, pandemonium struck among the thousands of protesters.