The Egyptian Health Ministry says 95 people died and hundreds were injured in the clashes. Egypt's interim president has declared a monthlong state of emergency.
In Cairo, smoke spread across the sky from fires smoldering in the streets where two sit-ins were largely abandoned, heaped with charred tent poles and tarps.
At the Rabaa Al-Awadiya camp, a protester said snipers were everywhere.
"People are dying — women, children," said Hesham Al Ashry, a pro-Morsi protester who follows hard-line Islamic ideology, speaking frantically from inside the sit-in.
Reports differed over the number of people killed and injured when security forces moved into the two sit-ins in the capital. Trains stopped operating and banks were closed as police chased protesters accused of instigating violence.
Most shops in Cairo shut their doors and the streets were almost entirely vacant of vehicles, which usually clog the capital.
"All the people are afraid," said taxi driver Korolos Gad, whipping his car through the empty streets and pointing out the military tanks that deployed in the city. "After a while, things will be fine."