Egypt's interim Vice President Mohamed ElBaradei has resigned his post following the killings, which were condemned by UN Secretary General as well as other world leaders and top Turkish officials.
The interim government has declared a one month state of emergency and curfew.
Curfew will begin at 21:00 at Egyptian local time, and will be enforced for a month as of Thursday between 19:00 pm and 06:00 am, according to Egypt state TV.
One of the two main pro-Morsi camps in Nahda Square has been cleared, while police tightens the noose on the other camp in Rabaa al-Adawiya Square.
Forces have stormed a field hospital in al-Adawiya camp and interfered in the treatment of dead bodies with the aim of concealing the death toll, spokesman Murat Ali has said.
Muslim Brotherhood leader Mohamed al-Beltagi has accused army chief Gen Abdel Fattah al-Sisi of dragging Egypt into a "civil war".
There are reports of clashes breaking out in several provinces across the country. Railways services have been halted.
Security forces moved in after dawn on Wednesday to disperse supporters of the deposed President Mohamed Morsi. Clashes were also reported in a third square in Cairo.
Civilian protesters are said to have been targeted by random shootings, while armored bulldozers removed barricades and tents put up on the edges of al-Adawiya camp.
Turkish Foreign Minister Ahmet Davutoglu urged Egypt's interim government to stop the crackdown immediately, describing it "unacceptable."
Two journalists were reported killed in clashes, while many were injured and several others, including two from the Anadolu Agency, were detained.
Several churches were targeted by arsonists, who threw fire-bombs at their facades, causing minor damage.
In the canal city of Suez, dozens of pro-Morsi supporters assembled outsize the Hamza Hospital and blocked Nasser Road with burning tires. Clashes left one dead and thirty injured.