Brotherhood officials said 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.
They said at least 120 were killed and more than 4,500 injured. Most victims in Rabaa Al-Adawiya were transported to the field hospital, leaving them unreported by health ministry hospitals, Ahram Online reported.
The health ministry, however, put the toll at 46 after clashes erupted following a night of massive rallies both for and against the ousted Islamist president. It said hundreds were wounded nationwide, including seven policemen.
Since yesterday eight people were killed in Egypt's second biggest city Alexandria, while 38 people died in the vicinity of Rabaa el-Adawiy Square, a health ministry official said. A 14-year-old boy was among the dead.
At least 708 people were injured, including 239 in the clashes in Nasr City and 469 other governorates.
The Interior Ministry today blamed the Muslim Brotherhood for deadly clashes and denied officers fired live rounds.
Interior Minister Mohamed Ibrahim said pro-Mursi sit-ins will be "dealt with soon".
"God willing, it will be broken up in a way that does not cause losses," Ibrahim said. "But, God permitting, it must end. We hope that they come to their senses...and join their political process.
"With regards to the timing...to disperse the protesters, there is complete coordination between us and the armed forces," Ibrahim told a news conference.