"The new toll from events outside the Republican Guard headquarters has risen to 51 dead and 435 wounded," Mohammed Sultan was quoted as saying by state news agency MENA.
The same emergency services had said earlier that 42 people died and 322 were wounded when shots were fired at the Muslim Brotherhood protesters.
The Muslim Brotherhood, which has led demonstrations against Wednesday's overthrow of Islamist president Mohamed Morsi, said its supporters were "massacred" by troops and police during dawn prayers in Cairo.
The military blamed "terrorists" while witnesses, including Brotherhood supporters at the scene, said the armed forces fired only warning shots and tear gas, and that "thugs" in civilian clothes carried out the shootings.
Jordan's Muslim Brotherhood said it "clearly showed the truth about the bloody military coup".
However the army-appointed interim president, Adly Mansour, set up a judicial commission of inquiry into the killings.
The conservative Islamist Al-Nur party, which won almost a quarter of the votes in 2011-2012 parliamentary elections and had backed the army's overthrow of Morsi, said it was pulling out of talks on a new government in response to the "massacre".
The bloodshed happened outside the headquarters of the elite Republican Guard, which the Brotherhood accuses of betraying Morsi, Egypt's first freely elected president.