US President Barack Obama has strongly condemned the violence in Egypt, and cancelled joint military exercises.
He said co-operation could not continue while civilians were being killed.
Egypt’s interior ministry has now authorised police to use live ammunition in attacks against them.
On Wednesday, security forces broke up Muslim Brotherhood protesters who were demanding the reinstatement of President Mohammed Morsi, with at least 500 people killed nationwide.
The Brotherhood members had been protesting for weeks about the army’s overthrow of Mr Morsi in July.
In the latest violence on Thursday, hundreds of Brotherhood members set fire to a government building near Cairo.
Local TV footage showed firefighters evacuating employees 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 Alexandria.
At least four Egyptian soldiers were shot dead by unknown gunmen near the city of el-Arish in the Sinai region.
The government says 525 people died nationwide on Wednesday, but the final toll is likely to be significantly higher.
Scores of bodies have not been registered, because the official count only includes bodies which have passed through hospitals.
The BBC has seen 202 bodies wrapped in shrouds at the Eman mosque, close to the main protest camp at Rabaa al-Adawiya Square.
Most of these are unlikely to have been counted in the official toll, and the BBC’s Middle East editor Jeremy Bowen says many had been burned beyond recognition.
The Muslim Brotherhood insists that more than 2,000 people died. It says 300 bodies were taken to the Eman mosque, and other bodies were taken to sports halls.
Reports speak of disputes between bereaved relatives and officials entrusted with documenting the causes of death.
Speaking from his holiday home in Martha’s Vineyard, 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 were being killed on the streets and rights were being rolled back.
He said that Egypt was on a dangerous path, and he called for it to reject violence and adopt a process of national reconciliation.
But he added: “We don’t take sides with any party or political figure.”
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”.
Wednesday’s violence began when armoured bulldozers moved into the two protest camps in Cairo, which had been occupied by pro-Morsi activists since soon 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.
Mr Morsi, Egypt’s first democratically elected president, was ousted by the military on 3 July.
He 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.