As Cairo counts its dead, peace remains remote

The smell of death hangs heavily in the air at Al-Iman Mosque in Nasr City. There are bodies as far as the eye can see and the blocks of ice laid on their chests to slow down the decomposition fight a losing battle with the intense summer heat.

Volunteers spray air freshener over the shrouded corpses in an attempt to mask the stench, but there is a point, as you first enter the makeshift morgue that in the past 24 hours doctors say has received nearly 350 bodies, where your knees go weak. Just for a moment.

Some of the bodies are charred beyond recognition, many were the victims of sniper fire to the head, others have gunshot wounds elsewhere on their bodies. Volunteers counted six children and four women among the dead.

The carpet is wet under feet from the melted ice, and stunned family members, their eyes red from weeping and glazed with grief, sit next to the bodies as large pedestal fans blow the fetid aroma of death mixed with air freshener in a sickening loop.

Outside an angry crowd has gathered - some are relatives clutching identification documents, desperate to get into the mosque and find their loved one, others are just despairing that what they felt was a peaceful protest was dispersed so violently by Egypt's security forces.

Every few minutes a group of men, wearing surgical masks, lift a body into a simple coffin. They then force their way through the crowd to the ambulances and cars waiting to transport the dead to better-equipped hospital morgues or to be buried in cemeteries all around Egypt.

Officially, the death toll from Wednesday's military action to clear the pro-Muslim Brotherhood protest camps in Cairo stands at 638, including 43 policemen, with more than 4200 wounded.

But volunteers at this mosque say the bodies that lie around us have not been counted or even recognised by Egypt's Health Ministry, which means the toll must surely rise in the coming days.

The Muslim Brotherhood says about 2600 of its supporters were killed when riot police and the military moved into their thousands-strong protests at Rabaa al-Adawiya Mosque in Nasr City and al-Nahda Square in Giza.

But in this critically divided country both sides are pointing fingers. Security forces claim the pro-Mursi protest camps were heavily armed, and say when they stormed Rabaa and al-Nahda they found the protesters' weapons stores.

The Brotherhood denies the claim, and says the military attacked its peaceful protests.

There is no doubt there were some who had weapons at the Brotherhood's protest camps, and when confronted by the security forces many fought back - by burning tyres and throwing rocks and petrol bombs at the police, or by arming themselves with pipes or sticks.

But human rights groups and Western governments say none of that is an excuse for the military's actions on Wednesday, when hundreds of soldiers and riot police backed by bulldozers and armoured personnel carriers fired tear-gas, bird shot and live ammunition at demonstrators who refused to give up their protest, leaving streets in flames and a steadily rising death toll.

The political and security crisis that now grips Egypt stretches way beyond its capital, to the heavily Christian populated cities of Minya and Sohag, to the critical seaport of Suez, to the restive North Sinai province, across the border into Israel and Gaza and all the way to Washington.

Burnt by promises from the Egyptian military that it would not use excessive force to clear the protest camps, US President Barack Obama announced the cancellation of joint military exercises with Egypt scheduled for next month.

While Obama still stopped short of calling the ousting of the democratically elected president Mohammed Mursi on July 3 a military coup, he said co-operation with Egypt could not continue while civilians were being killed.

Declining to declare the military's actions a coup meant the US President could avoid the potentially damaging cancellation of the $US1.3 billion ($1.4 billion) in aid the US provides to Egypt, which mostly goes to the military.

Overnight the United Nations Security Council was scheduled to meet to discuss the violence.

Unrepentant, Egypt's military-backed interim government stated on Thursday it would use live fire against protesters who attacked government buildings.

The announcement came as Egyptian television aired footage of supporters of Mursi torching two provincial government buildings in Giza, south of Cairo.

Equally defiant, Muslim Brotherhood leaders called for more mass protests in what is being described as a "Friday of Anger", even as so many of their supporters lay dead in Nasr City.

"It's not about Mursi any more. Are we going to accept a new military tyranny in Egypt or not?" the Brotherhood's spokesman Gehad el-Haddad told Reuters.

Meanwhile the Tamarod group, which collected the millions of signatures that led to the mass protests that overthrew the country's first democratically elected president, has urged people to set up neighbourhood watch groups to protect churches, government and private property.

Fairfax Media passed through one civilian checkpoint just before the dusk-to-dawn curfew imposed on the second day of the month-long state of emergency instigated by the interim government.

A small group of young men on motorbikes blocked an exit from the 15 of May Bridge, wielding handguns and a rifle. They allowed our car to pass only after reassuring themselves there were no Muslim Brotherhood supporters inside.

Adding to the worldwide condemnation of the Egyptian military's use of excessive force to clear the protests, a coalition of nine Egyptian human rights groups were united in their criticism of the failure of security forces to protect public security.

"That some participants in the sit-in and its leaders committed criminal acts, were in possession of weapons, and engaged in violence does not give the security authorities a licence to impose collective punishment and use excessive force when dispersing the sit-in."

And when choosing to use excessive force, the human rights groups said, decision-makers "did not show due consideration to containing retaliatory violence by the Muslim Brotherhood and its supporters".

Right now, every warring faction in Egypt has adopted the hardest line possible. Long-held prejudices against Islamists, Christians and secularists, as well as refugees from Palestine, Syria, and many African countries, have translated into open hatred.

More than 37 Christian churches, houses, monasteries, shops, and schools have been attacked and set on fire in Minya, while another five churches were destroyed in Assiut in upper Egypt, the Egyptian Organisation for Human Rights confirmed.

Violence continued in other smaller centres, as pro-Mursi supporters went on a rampage following the military's actions on Wednesday.

But it was not only churches that were attacked - Muslim Brotherhood protesters broke into Kirdasa police station, killed 11 police officers and mutilated the body of the station's commander, the human rights group said.

Amid such violence there is so little space for people to even mourn their dead, let alone work towards forming a new government.

The very idea of national reconciliation is inconceivable in an atmosphere of such intense divisions. But still the interim government is pushing on, drafting a new constitution and moving towards parliamentary and presidential elections in the next six months.

Yet all the Muslim Brotherhood supporters can see is a humiliating betrayal of their experiment with democracy, and yet more bloodshed.

As for the supporters of the military and its leader, General Abdel Fattah al-Sisi, whose picture is pasted all over many Cairo neighbourhoods, they sense a total victory over a long-distrusted foe and would be happy to erase the past year of Muslim Brotherhood-led government from the history books.

Dalia Ziada, the director of Ibn Khaldun Centre for Development Studies, described the mood in Egypt as "mad and sad".

"It is difficult now to speak about national reconciliation - we need first to retain stability and security and only then we will be able to sit and talk," Ziada said. "All the violence that is going on now makes it more and more complicated ... I am worried because people have started to look backwards, to say 'we are better off under military rule'.

"I do not want to end up with military rule ... I understand how urgent the situation is now, but I hope this will not be used to hijack the dream of having a civil, democratic state."

Back at al-Iman Mosque, Dr Hani Nowara was helping frantic relatives to identify their loved ones, with dozens of identification cards laid out on a lounge chair at the back of the room. He said from 7pm on Wednesday night until 6am on Thursday morning about 350 bodies had arrived from Rabaa - he had spent those hours cataloguing the injuries and trying to record a cause of death.

Surveying the chaotic scenes inside the mosque, he said the release of the bodies had been delayed by government attempts to bully relatives into signing documents claiming their loved one had died by suicide or in an accidental death.

"We got lawyers to come here, and now they are making sure the bodies are released as they should be."

Fairfax Media was unable to get a response to the allegations from the Egyptian Health Ministry before publication.

Nowara was philosophical about Egypt's future. "Egyptians have no other choice than democracy," he said.

Echoing the sentiments of the military and the interim government that formed in the wake of Mursi's overthrow, he said: "First we must ensure those who have committed the violence are brought to justice before a court, then we can start to sit and work together for Egypt."

But with both sides so far from each other, and amid an atmosphere of so much violence, the prospects of reconciliation appear depressingly remote.