Egyptian security forces shot dead dozens of supporters of the ousted president Mohamed Morsi shortly after the army chief called for a popular mandate to wipe out “violence and terrorism”. Men in helmets and black police fatigues fired on crowds gathered before dawn on the fringes of a round-the-clock sit-in near a mosque in north-east Cairo, a stronghold of the Muslim Brotherhood.

A Brotherhood spokesman, Ahmed Aref, said 66 people had been killed and another 61 were "brain dead" on life-support machines. Egypt's department of health said the official figure was 65 dead. More than 4,000 were treated for the effects of tear gas and gunshot or birdshot wounds, Mr Aref said. "Innocent blood was spilled," he said. "We have gone back 10 years."

Doctors working in nearby hospitals where the dead and wounded were taken described the shootings as a "catastrophe". Ahmed Fawzy, a cardiologist who was working at the field hospital in eastern Cairo, described it as a "crime against humanity."

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By early morning there were 28 corpses lined up around the walls of the makeshift morgue. Some had been shot by single bullets to the head, said doctors; others perished after live rounds passed through their necks or chest. More bodies were hauled in later, as supporters of Mr Morsi continued to clash with Egypt's central security services in the streets outside.

Doctors at the scene said they believed more than 100 people may have been killed. If initial estimates prove to be accurate, the massacre ranks as one of the worst single incidents of violence since the fall of Hosni Mubarak. Reports on al-Jazeera said that as many as 120 people may have been killed – a tally that chimes with testimony given to The Independent on Sunday from doctors at the scene.

Egypt's Interior Minister, Mohamed Ibrahim, later accused the Brotherhood of exaggerating the death toll for political ends and denied that police had opened fire. He said local residents living close to the Rabaa al-Adawiya mosque vigil had clashed with protesters in the early hours after they had blocked off a major bridge road, and that police had used tear gas to try to break up the fighting.

It was only three weeks ago that more than 50 supporters of Mr Morsi were shot dead by the military close to where the killings unfolded. Mr Ibrahim now appears to threaten a renewed assault on protesters, saying that, "God willing, soon" they will be "dealt with".

Clashes were continuing as police squared up against thousands of protesters close to the sit-in in Rabaa al-Adawiya, a suburb of eastern Cairo. Members of the central security forces fired sustained bursts of gunfire at protesters massing in the open road.

Supporters of Mr Morsi – who are demanding the Egyptian former leader be reinstated following a coup just over three weeks ago – cowered behind makeshift brick barricades as bullets fizzed overhead. Others ducked behind cars or ran for cover as live rounds ricocheted off walls.

In the field clinic, patients who had been shot with live rounds lay on the grubby, blood-stained floor as medics tried to treat their wounds. Eventually staff had to close the clinic when medical supplies dried up.

"I blame General al-Sisi," said one doctor, referring to Egypt's army chief and the man behind this month's popular coup. "They were killing us on his orders."

It is still unclear exactly how the fighting erupted. According to Gehad el-Haddad, a spokesman for the Brotherhood's political wing, it began on the fringes of the sit-in before dawn. Reports suggested that Mr Morsi's supporters had attempted to move beyond the rally's confines towards a nearby bridge, but were then beaten back by the central security services. One video uploaded on to YouTube seemed to verify that account, appearing to show a largely unprovoked line of police opening fire on demonstrators using tear gas.