World condemnation widened for the bloody crackdown on Morsi's mostly Islamist supporters, including an angry response from President Barack Obama, who canceled joint U.S.-Egyptian military maneuvers.
Violence spread Thursday, with government buildings set afire near the pyramids, policemen gunned down and scores of Christian churches attacked. As turmoil engulfed the country, the Interior Ministry authorized the use of deadly force against protesters targeting police and state institutions.
The Muslim Brotherhood, trying to regroup after the assault on their encampments and the arrest of many of their leaders, called for a mass rally on Friday in a challenge to the government's declaration of a monthlong state of emergency and a dusk-to-dawn curfew.
At least 638 people were confirmed killed and nearly 4,000 wounded in the violence sparked when riot police backed by armored vehicles, snipers and bulldozers smashed the two sit-ins in Cairo where Morsi's supporters had been camped out for six weeks to demand his reinstatement. It was the deadliest day by far since the 2011 popular uprising that overthrew autocratic ruler Hosni Mubarak and plunged the country into more than two years of instability.
Also on Thursday, The United Nations Security Council called on both the Egyptian government and the Muslim Brotherhood to exercise "maximum restraint" and end the violence spreading across the country. Council members called for national reconciliation.
The Health Ministry said that 288 of those killed were in the largest protest camp in Cairo's Nasr City district, while 90 others were slain in a smaller encampment at al-Nahda Square, near Cairo University. Others died in clashes that broke out between Morsi's supporters and security forces or anti-Morsi protesters elsewhere in the Egyptian capital and other cities.
Mohammed Fathallah, the ministry spokesman, said earlier that the blood-soaked bodies lined up in the El Iman mosque in Nasr City were not included in the official death toll. It was not immediately clear if the new figures included the ones at the mosque.
Inside the mosque-turned-morgue, the names of the dead were scribbled on white sheets covering the bodies, some of them charred, and a list with 265 names was plastered on the wall. Heat made the stench from the corpses almost unbearable as the ice brought in to chill the bodies melted and household fans offered little relief.
Weeping relatives filled the mosque courtyard and spilled into the streets. In a corner, a woman cradled the head of a slain man in her lap, fanning it with a paper fan. Nearby, an anguished man shouted, "God take revenge on you el-Sissi!" a reference to the powerful military chief, Gen. Abdel-Fatah el-Sissi.
Slumped over the body of his brother, Ihab el-Sayyed said the 24-year-old was getting ready for his wedding next week. "Last time I heard his voice was an hour or two before I heard of his death," he said, choking back tears.
Over the mosque speakers, announcements urged people to leave because their body heat was making the humid conditions worse inside the mosque, where posters of Morsi lay piled up in a corner.
Many people complained that authorities were preventing them from obtaining permits to bury their dead, although the Muslim Brotherhood announced that several funerals had been held Thursday. Fathallah denied that permits were being withheld.
"Bodies are getting decomposed. We only want to bury them. This is unfair," said Hamdan Abdullah, who had traveled from the city of Fayoum to retrieve the body of his niece.
Omar Houzien, a volunteer helping families search for their loved ones, said the bodies were carried to the mosque from a medical center at the protest camp in the final hours of Wednesday's police sweep because of fears they would be burned.
Elsewhere, a mass funeral was held in Cairo for some of the 43 security troops authorities said were killed in Wednesday's clashes. Interior Minister Mohammed Ibrahim, who is in charge of the police, led the mourners. A police band played solemn music as fire engines bore the coffins draped in white, red and black Egyptian flags in a funeral procession.
The deadly crackdown drew widespread condemnation from the Muslim world and the West.
Obama canceled joint U.S.-Egypt military exercises scheduled for next month, although he gave no indication that the U.S. planned to cut off its $1.3 billion in annual military aid to the country. The U.S. administration has avoided declaring Morsi's ouster a coup, which would force it to suspend the military aid.
"While we want to sustain our relationship with Egypt, our traditional cooperation cannot continue as usual when civilians are being killed in the streets and rights are being rolled back," the U.S. president said, speaking from his weeklong vacation in Massachusetts.
Obama said he also ordered his national security team to "assess the actions taken by the interim government and further steps that we may take as necessary with respect to the U.S.-Egyptian relationship."
Egypt's interim government issued a late night statement saying the country is facing "terrorist actions targeting government and vital institutions" by "violent militant groups." The statement expressed "sadness" for the killings of Egyptians and pledged to work on restoring law and order.
The statement also warned that Obama's position "while it's not based on facts can empower the violent militant groups and encourage them in its anti-stability discourse."
Egypt enjoys "full sovereignty and independence of its decision," the statement said.
The biennial Bright Star maneuvers, long a centerpiece of the deep ties between the U.S. and Egyptian militaries, have not been held since 2009, as Egypt grappled with the fallout from the revolution that ousted Mubarak. Morsi, a member of the Muslim Brotherhood, was elected president in 2012 during Egypt's first democratic elections.
Despite the curfew and state of emergency, violence spilled over to a second day Thursday.
The Interior Ministry said its decision to authorize police to use deadly force came after an angry crowd stormed the governor's office in Giza, the city next to Cairo that is home to the pyramids.
Associated Press reporters witnessed the burning buildings, a two-story colonial-style villa and a four-story administrative office on the road leading to the pyramids on the west bank of the Nile River.
"The ministry has given instruction to all forces to use live ammunition to confront any assaults on institutions or the forces," the statement read.
Egypt's military-backed government also pledged to confront "terrorist actions and sabotage" allegedly carried out by Muslim Brotherhood members.
State TV blamed Morsi supporters for the arson and broadcast footage showing firefighters evacuating employees from the larger building.
The Brotherhood's website IkhwanOnLine said thousands of Morsi supporters marched through Giza but were attacked by pro-military "militias." It did not say how the government buildings were set on fire.
Attackers also set fire to churches and police stations across the country for a second day Thursday.
In the country's second-largest city of Alexandria, Islamist protesters exchanged gunfire with an anti-Morsi rally, leaving scores injured, witnesses and security officials said. Attempts to storm police stations in the southern city of Assiut and northern Sinai city of el-Arish left at least six policemen dead and others injured.
Ishaq Ibrahim of the Egyptian Initiative for Personal Rights said his group had documented at least 39 cases of violence against churches, monasteries, Coptic schools and shops in different parts of the country on Wednesday.
Cairo, a city of some 18 million people, was uncharacteristically quiet Thursday, with only a fraction of its usually hectic traffic and many stores and government offices shuttered. Many people hunkered down at home for fear of more violence. Banks and the stock market were closed.
Fearful of more violence Friday in response to calls for more protests by both the Brotherhood and anti-Morsi camps, some main streets were closed and people in many neighborhoods set up cement blocks and metal barricades. Residents checked IDs in scenes reminiscent of the 2011 revolution when vigilante-style groups set up neighborhood watches to prevent looting and other attacks.
In Cairo's Nasr City neighborhood, smoke rose from the burned-out Rabaah al-Adawiya mosque compound that had been the epicenter of support for Morsi, its floor covered with black debris and nearby trees and grass charred. A makeshift field hospital was also gutted, its walls blackened and floors covered in pools of brackish water.
The turmoil is the latest chapter in a bitter standoff between Morsi's supporters and the interim leadership that took over the Arab world's most populous country following a July 3 coup. The military ouster came after millions of Egyptians took to the streets to demand Morsi step down, accusing him of giving the Brotherhood undue influence and failing to implement vital reforms or bolster the ailing economy.
Morsi has been held at an undisclosed location ever since. Other Brotherhood leaders, including several arrested Wednesday, have been charged with inciting violence or conspiring in the killing of protesters.
The Brotherhood has spent most of its 85 years as an outlawed group or enduring crackdowns by successive governments. The latest developments could provide authorities with the grounds to once again declare it an illegal group and consign it to the political wilderness.