Egypt's health ministry said it had registered 65 killed on Saturday in what the Muslim Brotherhood has described as an attack by the security forces on supporters of ousted Islamist President Mohammed Morsi in the capital Cairo.

Morsi's Muslim Brotherhood says 66 were killed and 61 were left "brain dead" in the attack. Hamdi Mahmoud, director of the health ministry press office, told Reuters that 65 had died, and a further nine were killed in overnight violence in Egypt's second city, Alexandria.

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 northeast Cairo, Morsi's Muslim Brotherhood movement said.

"They are not shooting to wound, they are shooting to kill," said Brotherhood spokesman Gehad El-Haddad. "The bullet wounds are in the head and chest."

Egyptian police fired tear gas to disperse supporters of deposed president Mohamed Morsi during a sit-in outside Cairo's Rabaa al-Adawiya mosque on Saturday. Egyptian police fired tear gas to disperse supporters of deposed president Mohamed Morsi during a sit-in outside Cairo's Rabaa al-Adawiya mosque on Saturday. (Fayez Nureldine/Getty Images)

They fell one by one, picked off by gunmen who aimed for the chest and head, witnesses said. Some of the dead, supporters of Morsi, were shot between the eyes.

In one of the bloodiest incidents since Morsi was removed from power by the army, the violence started around midnight with a barrage of teargas fired by police to drive his Muslim Brotherhood backers away from a major Cairo flyover.

By the time it ended some nine hours later, dozens lay dead, killed by what Mursi supporters described as a shooting spree by security forces lasting from dawn until about 9 a.m.

"It was like an execution," said Abdulrahman Ismail, 23, a Brotherhood activist who witnessed the violence

Interior Minister Mohammed Ibrahim said the Brotherhood was exaggerating the death toll for political ends, denied using lethal force and accused the Islamists of opening fire.

In the early stages of the violence, a Reuters journalist saw one policeman hit by gunshot. A security official said a dozen policemen were wounded by gunshots and rocks overall.

But the bodies piled up fast at the makeshift morgue in the Rabaa al-Adawiya protest camp where the Brotherhood has vowed to dig in until Morsi is reinstated as president. At 7:30 a.m. local time, a Reuters journalist counted 20 corpses covered by white sheets.

By the time the violence subsided, there were 36 in the blood-splattered room.

Other bodies were taken elsewhere: some two dozen went to a nearby hospital. Some of the dead were carried wrapped in blankets, others on planks of wood..

'It wasn't random gunfire'

The government appeared to receive a popular nod of approval for tougher action against the Brotherhood when hundreds of thousands took to the streets on Friday in response to army chief General Abdel Fattah al-Sisi's call for a protest against "violence and terrorism."

Protesters say there were snipers on rooftops aiming at people.Protesters say there were snipers on rooftops aiming at people. (Hassan Ammar/Associated Press)

But witnesses among the Brotherhood protesters said the military had not taken part in the night's violence, only the police, who are under the Interior Ministry, and thugs in plain clothes.

"It wasn't random gunfire," said Mahmoud Seif, 23, a Brotherhood activist who witnessed events unfold through the night and into the morning. "Two people died, one on either side of me. Both were hit in the head," he told Reuters at a clinic where the wounded were still coming in.

A Reuters cameraman filming the violence saw one youth fall to the ground after he was hit by gunfire and dozens more ferried away by ambulances during a half-hour spell of the shooting.

Dr. Ibtisam Zein, overseeing the Brotherhood morgue, said most of the dead were hit in the head, some between the eyes.

The trouble began when Brotherhood protesters approached the 6th of October Bridge — a flyover and major Cairo traffic artery. The minister said they had clashed with residents there, and that police fired teargas to separate the sides.

'The basic tactic of the police was to fire gas bombs, then stun grenades, then they would shoot birdshot.'—Ahmed El-Nashar, witness

Morsi supporters said the gas was accompanied by birdshot fire. For the next few hours, teargas and rocks flew as Mursi supporters faced off with the security forces along the highway near the site where Anwar Sadat was assassinated by Islamist gunmen in 1981.

Around dawn, the gunfire suddenly intensified, multiple witnesses in the Brotherhood protest camp said. "Man, people were just dropping," said Ahmed El-Nashar, a 34-year-old consultant, speaking English in an American accent.

"All the night it was running street battles — back and forth, back and forth," he said. "The basic tactic of the police was to fire gas bombs, then stun grenades, then they would shoot birdshot," he said.

"There were several dozen, maybe a hundred police in total, and several hundred plain-clothed men hurling rocks and firing home-made guns," he said. "There were snipers on the rooftops, I could hear the bullets whizzing past me."