"Clashes between the Egyptian army and pro-Morsi protesters at the Republican Guard headquarters have left at least 42 dead and 322 injured," the health ministry said.
The army arrested over 200 attackers, who were carrying guns, ammunition, and Molotov cocktails, according to the state-run MENA news agency.
The clash took place outside the the Republican Guard headquarters, where 61-year-old toppled president is said to have been put "under guard".
The statement said one army officer was killed and 40 soldiers were injured during the incident.
However, the Muslim Brotherhood contradicted army's statement, saying military opened fired on its supporters, killing several pro-Morsi protesters.
Meanwhile, prosecution shutdown the Cairo headquarters of the Muslim Brotherhood's Freedom and Justice Party after police recovered weapons from the building, media report said.
Morsi was toppled by the powerful military on Wednesday and kept under detention along with some senior aides of his Muslim Brotherhood party.
It urged "the international community and international groups and all the free people of the world to intervene to stop further massacres ... And prevent a new Syria."
At least 36 people were killed and more than 1,000 wounded in the violence during pro-Morsi protests on Friday. The military has deployed troops in Cairo and other locations.
Supporters and opponents of the ousted president are regularly organising rival demonstrations, with the former demanding Morsi's reinstatement and the latter supporting Morsi's overthrow.
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