After one of the most violent and bloody days in its modern history, Egypt faces a month-long state of emergency and overnight curfew, its interim government in crisis and citizens deeply divided.

By Thursday morning Australia time, the official death toll from the military crackdown on supporters of deposed president Mohamed Mursi stands at 638, and 4200 injured, according to the Egyptian Health Ministry. Human rights groups fear it will climb higher. About 43 policemen are understood to be included.

The UN Security Council will meet later on Thursday to discuss the situation after a meeting was requested by council members France, Britain and Australia.

As the fires burning at what was the protest camp the Rabaa al-Adawiya mosque in Nasr City burned well into the night, Cairo's usually jammed streets were deserted, shops shuttered.

And all over the country, communities were counting the cost of the past six weeks of political polarisation - churches were burned in the Upper Egypt cities of Minya and Sohag and as well as in Suez as sectarian violence spiked in the wake of the military's actions against the Muslim Brotherhood.

Clashes between pro- and anti-Muslim Brotherhood supporters broke out across Egypt - the largest toll was in Minya, about 250 kilometres south of Cairo, where health ministry officials said 41 people had died, six of them policemen.

Ten were killed in Alexandria, 15 in Ismailia 35 in Fayoum, while another five died in Suez when protesters tried to storm a government office, al-Jazeera reported.

The military's use of excessive force to clear the thousands-strong pro-Mursi protest camps - with bulldozers, tear gas, armoured personnel carriers and the firing of birdshot and live ammunition - was condemned by human rights groups, the United Nations and Western governments.

US Secretary of State John Kerry said the US ''strongly condemns today's violence and bloodshed across Egypt.'' Describing it as ''a serious serious blow to reconciliation and the Egyptian people's hopes for a transition towards democracy and inclusion'', Mr Kerry called for restraint and said the military and its interim government had a ''unique responsibility to prevent further violence''.

On Thursday, Australian Foreign Affairs Minister Bob Carr told ABC radio the events in Egypt were a ''tragic loss of life which Australia unreservedly condemns''. DFAT's travel advice is ''reconsider your need to travel''.

The US was reviewing the $US1.5 billion($1.65 billion) in aid it gives Egypt each year - most of which goes to the military - a spokesman for President Barack Obama said, adding the violence was ''directly counter to pledges from the interim government to pursue reconciliation'' with the Muslim Brotherhood.

It has consistently refused to label the actions to remove Dr Mursi as a coup as that would force it to suspend aid - a move many fear could bring an end to the Camp David accords that govern Egypt's often tense relationship with its neighbour, Israel.

Prime Minister Hazem Al Beblawi and Interior Minister Mohamed Ibrahim defended the crackdown, saying all other avenues had been exhausted.

''It was necessary to take a firm stand,'' Mr Beblawi said. ''When things spiral out of control, that's unacceptable.''

The National Salvation Front - a coalition of 11 political parties - also defended the action. It said the operation was ''a victory against all political forces trafficking in the name of religion'', alleging the Muslim Brotherhood bore ''full responsibility'' for the violence because its protests had not been peaceful.

But Vice-President Mohammed ElBaradei announced his resignation, saying he could not shoulder responsibility for ''bloodshed that could have been avoided''.

With AP, Judith Ireland, Reuters