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 Nasr City, in the city’s north-east.
“They are not shooting to wound, they are shooting to kill,” said Muslim Brotherhood spokesman Gehad el-Haddad. “The bullet wounds are in the head and chest.”
A Muslim Brotherhood website said 120 people had been killed and around 4,500 injured in the previous 48 hours.
More than 36 bodies were counted at one morgue, while health officials said there were a further 21 corpses in two nearby hospitals.
Activists rushed casualties into a makeshift treatment centre, while some were carried in on planks or blankets.
One teenager was laid out on the floor, a bullet hole in his head.
Interior minister Mohamed Ibrahim said only 21 had died and denied police had opened fire, accusing the Brotherhood of exaggerating the death toll for political ends.
Ibrahim said people living near to the Rabaa al-Adawia mosque vigil had clashed with protesters in the early hours after they had blocked a bridge. He said police had used tear gas to try to break up the fighting.
More than 200 people have been killed in clashes since the army toppled Morsi on 3 July, following protests against his year in power. The army denies staging a coup, saying it intervened to prevent national chaos.
Egypt, the largest state in the Arab world, with a population of 84 million, is battling economic woes and struggling with the transition to democracy two years after Hosni Mubarak was swept from power during the Arab Spring.
Hundreds of thousands of Egyptians poured on to the streets on Friday in response to a call by army chief General Abdel Fattah al-Sisi for nationwide demonstrations to give him backing to tackle the continued unrest.
His appeal was seen as a challenge to the Brotherhood, which organised its own rallies calling for the return of Morsi, who has been held in an undisclosed location since his ousting and now faces a range of charges, including murder. Yesterday it was revealed he is set to be transferred to the same Cairo prison where former leader Mubarak is being held.
Brotherhood leaders appealed for calm yesterday, but activists at the Rabaa al-Adawia mosque vigil remained aggrieved.
“The people want the execution of Sisi,” a cleric shouted to the crowd from a stage by the mosque. “The people want the execution of the butcher.”
Ibrahim said the pro-Morsi sit-ins would “God willing, soon be dealt with” based on a decision by a public prosecutor, who is reviewing complaints from local residents unhappy with the encampment on their doorstep.
The Brotherhood is a highly organised movement with grass-roots support throughout Egypt, making it hard to silence even if the army decides to crackdown. European Union foreign policy chief Catherine Ashton said she “deeply deplored” yesterday’s deaths and urged all sides to end the violence.
Witnesses said police first fired tear gas at Brotherhood protesters gathered on a boulevard leading away from the mosque, with live shots ringing out soon afterwards.
“There were snipers on the rooftops, I could hear the bullets whizzing past me,” said Ahmed el Nashar, 34, a business consultant. “People were just dropping.”
Dr Ibtisam Zein, overseeing the Brotherhood morgue, said most of the dead were hit in the head, some between the eyes.
The bodies were wrapped in white sheets and laid on the floor, their names scrawled on the shrouds. A cleaner mopped the floor, washing away pools of blood.
El-Haddad said the Brotherhood remained committed to peaceful protest, despite yesterday’s deaths. It is the second mass shooting of its supporters this month after security forces killed 53 people on 8 July.
Brotherhood activists at Rabaa said they would not be cowed and warned of worse bloodshed if the security forces did not back down. “We will stay here until we die, one by one,” said Ahmed Ali, 24, helping to treat casualties at the field hospital.
“We have the examples of Algeria and Syria in our minds. We don’t want it to become a civil war. If we take up arms it might become one.”