The army apparently opened fire on protestors that some reports say were praying in front of the army barracks where it is believed President Morsi is being held.

New York Times:

Egyptian soldiers opened fire on hundreds of supporters of ousted President Mohamed Morsi early Monday as they were praying before dawn outside the facility where he is believed to be detained, dozens of witnesses said.

At least 43 civilians were killed, all or most of them shot, and more than 300 wounded, doctors and health officials said. Security officials said one police officer died as well.

The attack marked a sharp escalation in the confrontation between the generals who forced out the president and his Islamist supporters in the streets.

Dozens of Islamists who had gathered to hold a vigil for Mr. Morsi denied there was any provocation for the attack. Two bystanders who had supported Mr. Morsi's ouster said that the demonstrators were unarmed and ran in terror as the attack began.

Bullet holes in cars, lampposts and corrugated metal barriers indicated that gunfire was coming from the top of a nearby building where the sandbag barriers around makeshift gun emplacements were visible. Bullet casings on the ground and collected by Islamist demonstrators bore the stamp of the Egyptian Army.

But Egyptian state television showed film of a pro-Morsi protester firing what appeared to be a homemade handgun at advancing soldiers from behind a corner about 250 yards away. The footage was in daylight, hours after the initial attack began.

A witness who lived nearby said he saw two men with similar weapons among the protesters.

The protesters, witnesses and video footage all appeared to portray the pro-Morsi demonstrators as attempting to fight back against the soldiers by throwing rocks.

Early in the morning, Egyptian state media sent out a news alert saying that an army lieutenant had been killed and 200 "armed individuals" were captured, then hours later reported that there were also dozens of civilian casualties.