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 nationwide 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 and bulldozers smashed the two sit-ins in Cairo where Morsi's mainly Islamist supporters had been camped out for six weeks calling for his reinstatement. It was the deadliest day by far since the 2011 popular uprising that toppled autocratic ruler Hosni Mubarak and plunged the country into more than two years of instability.
The Health Ministry said in a statement 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 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 Imam 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, many 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.
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 were 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 for victims who had been identified. Fathallah denied that permits were being withheld.
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 that they would be burned.
Elsewhere, a mass funeral was held in Cairo for some of the 43 security troops who 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 red fire engines bore the coffins draped in white, red and black Egyptian flags in a funeral procession.
Morsi's Muslim Brotherhood put the casualty toll at a staggering 2,600 killed and around 10,000 injured, but the figures appeared high in light of footage by regional and local TV networks, as well as The Associated Press.
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," he said, speaking from his weeklong vacation in Massachusetts.
Obama said the United States informed Egypt's interim leaders Thursday morning about plans to cancel the military exercises. The president 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."
The Bright Star maneuvers, long a centerpiece of the deep ties between the U.S. and Egyptian militaries, were scheduled to have lasted about three weeks. Several other countries, including Turkey, Jordan and Britain, have also participated.
The U.S. and Egypt have not held the biennial exercises since 2009, as Egypt grappled with the fallout from the revolution that ousted its longtime autocratic leaders Hosni 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 in Giza a two-story colonial-style villa and a four-story administrative building, located on the road that leads 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 in a statement 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 as several attempts by the Muslim Brotherhood devolved into violence.
The Brotherhood also called for protests on Friday, saying they would grow in intensity.
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.
Wednesday's violence started with riot police raiding and clearing out the two camps, sparking clashes there and elsewhere in the Egyptian capital and other cities.
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.
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. The military ousted Morsi after millions of Egyptians massed in the streets at the end of June to call for him to 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 since July 3. 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 the 85 years since its creation 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.
Obama on Egypt
Chilmark, Mass. • President Barack Obama has scrapped joint U.S.-Egypt military exercises scheduled for next month, saying American cooperation with the Egyptian government cannot continue when civilians are being killed in the streets. He directed his national security team to see what additional steps the U.S. might take going forward.
Obama spoke from Martha's Vineyard in Massachusetts, where he is on vacation.
The Bright Star military exercise has been a centerpiece of the two countries' military relations for decades.