US president stops short of suspending military aid as clashes between security forces and Brotherhood supporters rage on

Egyptian security forces clashed with supporters of the Muslim Brotherhood for a second day on Thursday as muted international condemnation led by Barack Obama failed to quell violence now said to have killed at least 638 people and wounded many thousands more.

The death toll from the ongoing crackdown is likely to be far higher, with many bodies remaining unaccounted for in mosques near the scene of the two major assaults on Brotherhood sit-ins on Wednesday.

The violence achieved its aim of clearing both protest sites but led to widespread rage and revenge attacks by supporters of the Brotherhood who torched a number of government buildings.

In the early hours of Friday the Brotherhood called for a nationwide "millions' march of anger" after noon prayers, Reuters reported.

"Despite the pain and sorrow over the loss of our martyrs, the latest coup makers' crime has increased our determination to end them," the Islamist group said in a statement.

In a counter move, a loose liberal and leftist coalition, the National Salvation Front, called on Egyptians to protest on Friday against "obvious terrorism actions" conducted by the Brotherhood.

The government warned it would turn its guns on anyone who attacked the police or public institutions after protesters torched a government building in Cairo on Thursday.

Responding to the army's brutal crackdown on protesters, Obama announced the cancellation of joint US military exercises with Egypt in a carefully calibrated rebuke that stopped short of a more significant suspension of aid.

The US president interrupted his family vacation on Martha's Vineyard to condemn the bloodshed, but stressed that any move toward peaceful democracy was a difficult process that could take decades.

"We appreciate the complexity of the situation," he said. "We recognise that change takes time. There are going to be false starts and difficult days. We know that democratic transitions are measured not in months or even years, but sometimes in generations."

Egypt's presidency said early on Friday Obama's remarks were not based on "facts" and would strengthen and encourage violent groups, Reuters reported.

His statement disappointed many in the diplomatic community who had hoped for a suspension, or even cancellation of $1.3bn in annual US military aid to Egypt, but the administration is anxious to retain this link for future leverage over the generals.

"If I'm an Egyptian general, I take notice and think President Obama is trying to take the least painful step to demonstrate to various constituencies in the US that he means what he says about democracy in Egypt," said Amy Hawthorne, who until recently was an Egypt policy official at the State Department. "But only the least painful step, so we won't take him that seriously."

The White House's limited intervention came as clashes took place for a second day in the capital Cairo, where an angry crowd stormed a security building in Giza and sporadic fighting was reported in at least four other parts of the country, including central Egypt where at least one police station and several churches were torched.

In Beni Suef, a southern city, locals said demonstrators attacked the security headquarters and a Coptic school. In Ismaïlia, a city near the Suez Canal, protesters backing the ousted president Mohamed Morsi attempted to attack a police station with a car, while Brotherhood members held a protest after the start of the evening curfew.

Overall, though, violence was markedly lower than on Wednesday – a day that appeared to be worse than the fears of some politicians and even Brotherhood backers, who had been bracing for an imminent attack on their hubs in north-eastern and western Cairo.

Bodies were still being counted in three mosques, three hospitals and two morgues, said Brotherhood spokesman Gehad el-Haddad early on Thursday, hours after a major assault led by interior ministry forces left behind scenes of shocking carnage at two sites used by supporters for the past six weeks.

Morgue officials struggled to cope with the number of bodies arriving at the premises. As a result, dozens of decaying bodies lay in coffins outside, relatives piling them with ice to stop the rot. Many claimed the police had refused to record their deaths as murder.

By daybreak, both protest sites were ravaged wastelands. Throughout Thursday, cleaners picked through the wreckage-strewn remains of the sites in an attempt to create a sense of normality. Protesters who had been encamped there had all fled or been arrested. Several groups made symbolic attempts to establish new hubs elsewhere in Cairo, but Brotherhood leaders continued to call on supporters to refrain from violence and hold only peaceful demonstrations.

Meanwhile, Egypt's military-backed interim government remained defiant, pledging in a statement to confront "terrorist actions and sabotage", laying the blame for the violence at the feet of the Brotherhood.

"The cabinet expressed its determination to confront the terrorist actions and sabotage by elements of the Muslim Brotherhood organisation," it said. "These actions are carried out as part of a criminal plan that clearly aims at toppling the state." State television quoted the interior ministry as saying the security forces would again use live ammunition to counter any attacks against themselves or public buildings.

The curfew that had been announced in a declaration of emergency that was imposed across the country for 30 days will now be imposed from 9pm to 6am.

In the street outside Cairo's Zeinhom morgue, families of victims vowed to resist the new curfew, refusing to leave the street until their relatives' bodies were accepted by the mortuary. "Curse the curfew," said Atef Fatih, whose brother was shot dead on Thursday. "We don't care about it. We will wait until they let the body inside."

Brotherhood leaders warned they could not restrain the anger of supporters across the country and said they feared the outbreak of more widespread violence in coming weeks as the full scale of the massacre in Cairo sinks in.

Christian leaders said that violence against Egypt's minority Coptic community was now at its highest for many decades. Islamists have angrily denounced Egypt's Christians as having given political cover to the new government, which was ushered into power by military chief, General Abdel Fatah al-Sisi, who ordered his officers to arrest Morsi and his aides on 3 July.

The six-week standoff between the state and the Brotherhood failed to reach any form of compromise, setting the scene for the violent clashes of this week. Brotherhood leaders had persistently said that the protest sites in Cairo would remain peaceful. Two earlier assaults by security forces had led to an estimated 300 deaths.

Morsi has been held incommunicado on a military base throughout the crisis. He is understood to have threatened to start a hunger strike should security forces carry through with their threat to attack both protest sites.