An Egyptian Health Ministry spokesman said the death toll in violence outside the Cairo headquarters of the Republican Guard stood at 42, with 322 people injured after the Muslim Brotherhood accused the security forces of attacking protesters there, NBC News reported on Monday.
The Egyptian military said "a terrorist group" had tried to storm the building. A military source described the attackers as "armed Muslim Brotherhood elements", saying they had tried to storm the building at dawn.
The bloodshed deepened Egypt's political crisis, escalating the struggle between the army, which overthrew Morsi last Wednesday after mass demonstrations demanding his resignation, and the Brotherhood, which has denounced what it called a coup.
As an immediate consequence, the ultra-conservative Islamist Nour party, which initially supported the military intervention, said it was withdrawing from stalled negotiations to form an interim government for the transition to fresh elections.
Al Jazeera's Egypt news channel broadcast footage of what appeared to be five men killed in the violence, and medics applying cardiopulmonary resuscitation to an unconscious man at a makeshift clinic at a nearby pro-Morsi sit-in.
A Reuters television producer at the scene saw first aid helpers attempting mouth-to-mouth resuscitation on a dying man. Wounded people were being ferried to the field hospital on motorbikes, given first aid treatment and taken away in ambulances.
The military overthrew Morsi on Wednesday after mass nationwide demonstrations led by youth activists demanding his resignation. The Brotherhood denounced the intervention as a coup and vowed peaceful resistance.
Military vehicles sealed off traffic in a wide area around the Rabaa Adawia mosque where Morsi supporters led by senior Brotherhood leaders have been staging protests since his ouster.
The army also closed two of the main bridges across the Nile River with armoured vehicles, witnesses said.
Talks on forming a new government were already in trouble before Monday's shooting, after the Nour party rejected two liberal-minded candidates for prime minister proposed by interim head of state Adli Mansour.