The Egyptian people had spent their first night under curfew as a month-long state of emergency was declared across the country, following violent scenes that left hundreds dead and many more seriously injured.

The Independent's correspondent Alastair Beach was at the Al Eman mosque in Nasr City where at least 242 bodies are being held. The official countrywide total death toll is now 525, although this could be higher.

Hundreds of supporters of Egypt's Muslim Brotherhood stormed a government building in Cairo and set a fire at its entrance, state TV and witnesses said.

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And today President Barack Obama announced he would cancel joint military exercises with Egypt next month and said the United States "strongly condemns" the violent crackdown on Muslim Brotherhood supporters.

He said he had to cancel the exercises because "Our traditional cooperation cannot continue as usual."

Speaking from Massachusetts, the President still refused to label the take-over a coup, which would involve cutting off the $1billion in aid Egypt receives from America a year.

He stressed that the US "cannot determine the future of Egypt, as it was "a task for the Egyptian people".

"We don't take sides with any particular party or political figure", he added.

Muslim Brotherhood spokesperson Gehad El-Haddad announced today that two of the group's leaders were shot when police raided two protest camps in Cairo of supporters of deposed President Mohamed Mursi on Wednesday, killing hundreds of people.

He said the the bloodshed has made it more difficult for the Brotherhood to persuade its members to continue on a path of peaceful resistance to the interim government.

“After the blows and arrests and killings that we are facing emotions are too high to be guided by anyone,” he said.

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He also said the group were struggling to locate members. “We can't confirm the whereabouts of all of them [brotherhood leaders] yet. Two of the top leaders have been shot but are not dead as far as I know. About six of them have lost their sons and daughters,” he said. “It's a bad blow, a very strong blow.”

As the 7pm local time to 6am curfew ended this morning, the Brotherhood had vowed to bring down the “military coup” whilst remaining committed to peaceful activism after security officials cleared protest camps filled with supporters of ousted President Mohamed Morsi.

Egypt's Muslim Brotherhood had said it would march through Cairo. “Marches are planned this afternoon from Al-Iman mosque to protest the deaths,” the Islamist group said in a statement.

In Alexandria, Egypt's second biggest city, protesters were already on the move by early afternoon.

Meanwhile, authorities announced this morning that the 84 people will face military prosecutors on charges of murder and burning churches, according to the countries state news agency.

Interim Prime Minister Hazem el-Beblawi said in a televised address to the nation that it was a "difficult day" and that he regretted the bloodshed but offered no apologies for moving against Morsi's supporters, saying they were given ample warnings to leave and he had tried foreign mediation efforts.

At the site of one Cairo sit-in, garbage collectors cleared still-smouldering piles of burnt tents on Thursday. Soldiers dismantled the stage at the heart of the protest camp. A burnt out armoured vehicle stood abandoned in the street.

Yesterday’s bloodshed ensued after Egypt’s military led interim government forcibly broke up the Rabaa al-Adawiya camp in northeast Cairo and another camp near Cairo University on Thursday, opening fire at crowds of protesters.

Hundreds of people died in the crackdown and nationwide clashes ensued.

Interim Vice President and Nobel laureate Mohamed el-Baradei resigned in protest over the events now widely referred to as a massacre. In a statement announcing his resignation, he said: "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."

Brotherhood spokesman Gehad El-Haddad took to Twitter to vow that their Islamist organisation would remain "non-violent and peaceful." "We remain strong, defiant and resolved,” said. “We will push (forward) until we bring down this military coup.”

Traffic has now started flowing back through the area of Cairo where supporters of the deposed president set up a protest camp at the heart of a power struggle between Islamists and the army-backed government, according to a Reuters witness.

Official reports from Egypt’s Health Ministry state 460 civilians were killed, along with 43 police officers. Spokesman Khaled el-Khateeb told The Associated Press this morning that the number of injured in the previous day's violence has also risen to 3,572.

He says the ministry was in the process of updating the latest figures and that an even higher death toll was likely. were injured. The Muslim Brotherhood however argues that the death toll is already much higher at 2000.

The military's violent measures were widely condemned across the globe, with US Secretary of State John Kerry describing the army’s action as “a serious blow” to all reconciliation efforts, and Prime Minister David Cameron stressing that the violence is “not going to solve anything”.

Turkish Prime Minister Tayyip Erdogan called on the EU to convene, having condemned Western nations for failing to intervene before civilians were killed.

"Those who remain silent in the face of this massacre are as guilty as those who carried it out. The U.N. Security Council must convene quickly," Erdogan told a news conference in Ankara.

"I am calling on Western countries. You remained silent in Gaza, you remained silent in Syria ... You are still silent on Egypt. So how come you talk about democracy, freedom, global values and human rights," he said.