The interim Egyptian government now says 525 people died and 3500 were injured in violence across the country on Wednesday. It says the dead include 43 policemen.
The violence, the bloodiest day since the revolution two years ago, was sparked by military action to clear anti-government protest camps in Cairo.
The Muslim Brotherhood, the party of ousted president Mohammed Morsi, says the real death toll is nearer 2000.
The Egyptian government has declared a state of emergency, the BBC reports, with an overnight curfew in Cairo and other cities between 7pm and 6am.
The Army is to help police maintain security, with interim prime minister Hazem Beblawi saying security has to be restored.
In a televised address, he expressed regret for the loss of life and said the state of national emergency would be lifted as soon as possible.
Interior minister Mohammed Ibrahim says members of the Muslim Brotherhood have been arrested and are being interrogated. He says the protest sites had been infiltrated by armed gangs.
Armoured bulldozers moved deep into the main protest camp outside the Rabaa al-Adawiya mosque in Cairo shortly after dawn on Wednesday morning. Another camp, at Nahda Square, was also cleared.
Supporters of Mr Morsi had been at the camps since he was deposed by the Army on 3 July. Rumours of a clearance by the Army had been circulating since Monday.
The BBC reports the streets of Cairo are eerily quiet now.
Liberal quits govt
Interim vice-president Mohammed El Baradei announced his resignation on Wednesday. The liberal leader was previously one of the leading public faces of the new regime.
"I cannot continue in shouldering the responsibility for decisions I do not agree with and I fear their consequences. I cannot shoulder the responsibility for a single drop of blood," he said in a statement.
Mr El Baradei was among those consulted by the Army when it organised the overthrow of Mr Morsi. He was formerly the head of the International Atomic Energy Agency.
International reaction
Turkish Prime Minister Tayyip Erdogan has called on the United Nations Security Council to convene quickly and act after what he described as a massacre in Egypt.
Mr Erdogan says those who remain silent in the face of this massacre are as guilty as those who carried it out.
French president Francois Hollande has summoned the Egyptian ambassador in France to a meeting while Denmark has suspended funding for two development projects run with the Egyptian government.
But the United Arab Emirates and Bahrain say they understand the Egyptian government's need to restore order.
American Secretary of State John Kerry has called on the authorities to lift the state of emergency.
Senator Kerry says the events have dealt a serious blow to Egypt's political reconciliation efforts.
He says all Egyptians - both in and out of government - need to take a step back and help calm the situation.
The senator says this is a pivotal moment for all Egyptians.
