Two churches were attacked and set on fire in Dermous, while an air force colonel and a military conscript were killed in an attack on a highway, security sources said.
Among the dead in Cairo were Asmaa Beltagy—the 17-year-old daughter of Mohammed Beltagy, one of the Muslim Brotherhood's top leaders—and two foreign media journalists.
American nationals were among 543 people arrested during the camp clearances, security sources said. Hundreds of weapons were confiscated.
Pro-Morsi protesters were seen throwing stones and Molotov cocktails at troops, Reuters reported. Security sources said six police officers were killed and 12 injured during the operation. The interior ministry said only tear gas had been used to clear the camps, but a Reuters reporter said he saw about 20 protesters who had been shot in the legs by soldiers.
(See more: Scenes from the turmoil in Egypt)
Eyewitness Ahshur Abid told Reuters he saw at least 15 bodies at a field hospital beside the sprawling Rabaa camp.
"It is nasty inside, they are destroying our tents. We can't breathe inside and many people are in hospital," volunteer Murad Ahmed told a Reuters correspondent at the camp, where Muslim Brotherhood officials had positioned sandbags in anticipation of a police raid.
United Nations Secretary General Ban Ki-moon condemned the violence used by Egypt's security forces.
"While the UN is still gathering precise information about today's events, it appears that hundreds of people were killed or wounded in clashes between security forces and demonstrators," he said in a statement.
At one stage, state television reported that armed protesters were inside Cairo Zoo, near the Nahda camp, firing at police. An explosion heard at the zoo gate, followed by fire, it said.
Turkey's prime minister called on the United Nations Security Council to help, describing Wednesday's events as a "massacre."
"The international community, especially the U.N. Security Council and Arab League, must act immediately to stop this massacre," Tayyip Erdogan's office said in a statement.
(Read more: Violence doesn't shake up Egyptian stock market)
The sit-in camps were formed in protest at the military-backed July 3 ouster of democratically elected Morsi. More than 300 people have already died in political violence since the army deposed Morsi exactly 12 months into his four-year term as president.
On Tuesday, police fired tear gas at Morsi supporters who marched on the country's Ministry of Religious Endowment.
NBC News' Alastair Jamieson, Reuters and The Associated Press contributed to this report.