Army troops did not take part in the two operations, but provided security at the locations. Police and army helicopters hovered over both sites hours after the police launched the simultaneous actions shortly after 7 a.m. (0500 GMT).
The Health Ministry said 149 people were killed and 1,403 injured across Egypt, but it did not immediately provide a breakdown.
An alliance of pro-Morsi groups said Asmaa Mohammed el-Batagy, the 17-year-old daughter of the senior Brotherhood figure who was detained by police, was shot and killed. Her brother, Ammar, confirmed her death on his Twitter account.
Two journalists were among the dead -- Mick Deane, 61, a cameraman for British broadcaster Sky News, and Habiba Ahmed Abd Elaziz, 26, a reporter for the Gulf News, a state-backed newspaper in the United Arab Emirates, the news organizations reported. Both had been reported to be shot.
A security official said 200 protesters were arrested at both sites. Several men could be seen walking with their hands up as they were led away by black-clad police.
The Muslim Brotherhood's political arm claimed that more than 500 protesters were killed and some 9,000 wounded in the two camps, but those figures could not be confirmed and nothing in the video from AP or local TV networks suggested such a high death toll.
Before he was detained, Mohammed el-Beltagy put the death toll at more than 300, urged police and army troops to mutiny, and said Egyptians should take to the streets to show their disapproval of the crackdown.
"Oh, Egyptian people, your brothers are in the square. Are you going to remain silent until the genocide is completed?" said el-Beltagy, who is wanted by authorities to answer allegations of inciting violence.
Police fired tear gas elsewhere in Cairo to disperse Morsi supporters who wanted to join the Nasr City camp after it came under attack. State TV also reported that a police captain had been abducted by Morsi supporters in the area, but there was no official statement about that.
Islam Tawfiq, a Brotherhood member at the Nasr City sit-in, said the camp's medical center was filled with dead and that the injured included children.
"No one can leave and those who do are either arrested or beaten up," he told AP.
Security officials said train services between northern and southern Egypt were suspended to prevent Morsi supporters from traveling to Cairo. Clashes erupted on two roads in the capital's upscale Mohandiseen district when Morsi supporters opened fire on passing cars and pedestrians. Police used tear gas to chase them away.
The security officials spoke on condition of anonymity because they were not authorized to talk to media.
Churches belonging to Egypt's minority Coptic Christians were torched in four provinces south of Cairo -- Minya, Assiut, Sohag and the desert oasis Fayoum. In the city of Bani Suef south of Cairo, protesters set three police cars on fire. Farther south in the Islamist stronghold of Assiut, police used tear gas to disperse pro-Morsi crowds in the city center.
Morsi supporters want him reinstated and are boycotting the military-sponsored political process, which includes amending the Islamist-backed constitution adopted last year and holding parliamentary and presidential elections early next year.
The U.S. gave a stern warning to Egypt's leaders, with Kerry condemning the violence as well as the restoration of emergency rule. He urged them to calm the situation.
"This is a pivotal moment for all Egyptians," said Kerry, who spoke by phone with the foreign minister. "The path toward violence leads only to greater instability, economic disaster and suffering."
Turkish Prime Minister Recep Tayyip Erdogan's office called it "a serious blow to the hopes of a return to democracy," while Iran warned that the violence "strengthens the possibility of civil war."
British Prime Minister David Cameron, who also condemned the violence, called for "a genuine transition to a genuine democracy. That means compromise from all sides -- the President Morsi supporters but also the military."
U.N. Secretary-General Ban Ki-moon urged all Egyptians to focus on reconciliation, while European Union foreign policy chief Catherine Ashton said dialogue should be encouraged through "peaceful protest, protecting all citizens and enabling full political participation."
At least 250 people have died in previous clashes since the coup.
Morsi, Egypt's first freely elected president, had just completed a year in office when he was toppled. He has largely been held incommunicado but was visited by Ashton and an African delegation.
Several bids by the U.S., the European Union and Gulf Arab states to reconcile the two sides in Egypt in an inclusive political process have failed, with the Brotherhood insisting that Morsi must first be freed along with several of the group's leaders who have been detained in connection with incitement of violence.
The trial of the Brotherhood's leader, Mohammed Badie, and his powerful deputy, Khairat el-Shater, on charges of conspiring to kill protesters is due to start later this month. Badie is on the run, but el-Shater is in detention. Four others are standing trial with them on the same charges.