Brotherhood officials said the security forces started firing shortly before pre-dawn prayers on protesters staging a sit-in here in support of Morsi, Egypt's first democratically elected president who was toppled by the military on July 3.
The Islamist group, which 61-year-old Morsi formerly headed, insisted that 75 of its supporters were killed and the figures are expected to rise as hundreds more were injured.
However, the Heath Ministry published a conflicting death toll, putting the figure at 19.
A doctor at a field hospital close to the protest at the Rabaa al-Adawiya mosque told the BBC that more than 1,000 people had also been injured.
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A security source told state-run news agency MENA that 53 Brotherhood members were arrested for wielding arms.
Morsi, who is facing several criminal charges, was last seen in public on June 26 and has been detained along with senior aides of his Muslim Brotherhood party.
Both pro- and anti-Morsi supporters had been holding huge protests overnight in the capital, with some supporting army and others angrily demanding his return to power.
Earlier, army chief Abdel Fattah El-Sisi had asked people to come on street to give him a mandate to confront "violence and terrorism".
Clashes also broke out in Upper Egypt's Luxor and Mahalah, located in the Delta governorate of Gharbiya.
In the Nile Delta city of Gharbiya, 10 people - including a police officer - were injured in clashes between loyalists and opponents of Morsi yesterday.