An Egyptian Health Ministry official says 35 people have been killed in an attack outside the headquarters of the Republican Guard in Cairo. State TV later reported that the death toll had risen to 42.
Khaled el-Khatib said Monday that initial reports indicated 35 people were killed and 300 wounded in shooting outside the building.
The Muslim Brotherhood are calling for an uprising across Egypt.
The Egyptian military said "a terrorist group" had tried to storm the building. One army officer had been killed and 40 wounded, the military said.
Earlier, medical sources said at least 15 people were killed, when the Muslim Brotherhood said shots were fired at supporters of deposed President Mohamed Morsi near the military building where he is being held.
Murad Ali of the Brotherhood's Freedom and Justice Party said 34 Morsi supporters had been killed. He said shooting broke out in the early morning while Islamists staged a sit-in outside the Republican Guard barracks.
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 spokesman for Morsi's Muslim Brotherhood said its members were unarmed and were fired upon while praying outside the building.
This is the largest death toll from a single incident in Egypt since the ouster of Hosni Mubarak in 2011.
The Islamist Al-Nour party, which backed Morsi's ouster, called the incident a "massacre" and announced it will not take part in any political negotiation.
On Sunday night, opponents of Egypt's deposed Islamist President Mohamed Morsi packed Tahrir Square in the tens of thousands to show the world his ouster was not a military coup but the reflection of the people's will.
The Tahrir gathering was staged as a counter-demonstration two days after Islamist rallies exploded into deadly violence, the protest raised the stakes as the country's interim leaders struggled to put together a new government.
As the crowds grew, wave after wave of military aircraft skimmed over the capital, with one formation leaving behind long trails of smoke in black, white and red – the colors of the Egyptian flag.
"We are on the street to show the world that it was a popular revolution and not a coup that overthrew" Morsi on Wednesday, said a beaming teacher who gave her name as Magda.