The UN Security Council has urged all parties in Egypt to exercise “maximum restraint”, after an emergency meeting.
This comes a day after least 638 people were killed when security forces broke up the camps of protesters allied to the Muslim Brotherhood.
The protesters had been demanding the reinstatement of President Mohammed Morsi, overthrown by the army in July.
Meanwhile, Egypt’s presidency said US President Obama’s condemnation of the crackdown was “not based on facts”.
“We deplore violence against civilians, ” said Barack Obama, adding that joint military exercises with the Egyptian army were being cancelled.
He said co-operation could not continue while civilians were being killed. However, he stopped short of cutting the $1.3bn (£830m) in aid, which the US gives to Egypt.
But Egypt’s presidency said the US leader’s reaction “may encourage violent armed groups”.
Egypt is currently in a state of emergency. The interior ministry has given police authorisation to use live ammunition in self-defence or when dealing with attacks on government buildings.
Many areas are affected by night-time curfews. The US has warned its citizens not to travel to Egypt, and says those already there should leave.
“The view of council members is that it is important to end violence in Egypt and that the parties exercise maximum restraint,” said Argentina’s ambassador to the UN, Maria Cristina Perceval, after the security council met on Thursday evening.
“The members first of all expressed their sympathy to the victims and regretted the loss of lives,” she said.
Earlier in the day, in the latest violence, hundreds of Brotherhood members set fire to a government building near Cairo.
Local TV footage showed firefighters bringing employees out from the building – which housed the offices of the Giza local government.
State-run Nile News TV also reported clashes between Brotherhood members and residents in a suburb of Egypt’s second city, Alexandria.
Seven Egyptian soldiers were shot dead by unknown gunmen near the city of El Arish in the Sinai region, according to security forces.
Death toll differences
The government says 638 people died nationwide on Wednesday, but the final toll could be higher.
Earlier on Thursday, there were heated disputes between bereaved relatives and officials entrusted with documenting the causes of death, because the official death toll only includes bodies which have passed through hospitals.
Many other bodies were laid in mosques or schools halls, like the 202 bodies which the BBC saw at the Eman mosque close to the main protest camp at Rabaa al-Adawiya Square.
Most of these are unlikely to have been counted – at least initially – in the official death toll.
The BBC’s Middle East editor Jeremy Bowen says many of the bodies have been burned beyond recognition.
Speaking from his holiday home in Massachusetts, Mr Obama condemned the interim Egyptian government’s actions in ordering security forces to break up the protest camps.
Announcing the cancellation of joint military exercises scheduled for later this month, he said co-operation with Egypt could not continue as normal while civilians’ rights were being rolled back.
He said Egypt was on a dangerous path and urged the government to reject violence and adopt a process of national reconciliation.
But he added: “We don’t take sides with any party or political figure.”
US Defence Secretary Chuck Hagel confirmed the US would retain its military ties with Egypt. But he said the violence was putting “important elements of our longstanding defence co-operation at risk”.
Other international figures have also condemned Wednesday’s violence.
Navi Pillay, the UN High Commissioner for Human Rights, has demanded an independent, impartial inquiry into what happened.
“The number of people killed or injured, even according to the government’s figures, point to an excessive, even extreme, use of force against demonstrators,” Ms Pillay said in a statement.
Turkish Prime Minister Recep Tayyip Erdogan described the events as a “very serious massacre”.
French President Francois Hollande summoned Egypt’s ambassador to France and said that “everything must be done to avoid a civil war”.
Wednesday’s violence began when armoured bulldozers moved into the two Cairo protest camps, occupied by pro-Morsi activists after he was ousted on 3 July.
The smaller of the two protest camps, at Nahda Square, was cleared quickly but clashes raged for several hours in and around the main encampment at Rabaa al-Adawiya. The mosque of the same name was damaged by fire.
Mobs later carried out reprisal attacks on government buildings and police stations as well as churches belonging to the country’s Coptic Christian minority.
In a televised address on Wednesday evening, Egyptian interim Prime Minister Hazem Beblawi defended the operation, saying the authorities had to restore security.
He declared a state of emergency, but said this would be lifted as soon as possible.
A dawn-to-dusk curfew is in force in Cairo and much of the rest of the country.
Mr Morsi, Egypt’s first democratically elected president, is now in custody, charged with murder over a 2011 jailbreak. His period of detention was extended by 30 days on Thursday, state media said.