The killings have reinforced fears about bloodshed in the aftermath of Mr. Morsi’s removal.
The supporters of the ousted president said they want him returned to power.
At least three supporters of the ousted President of Egypt, Mohammed Morsi, were killed Friday after the army opened fire on a crowd that surged towards a military compound where Mr. Morsi is believed to be held.
There were initial conflicting details of the number of those killed with reports saying at least one person was killed. Aljazeera television said at least three died while many sustained injuries from the bullet fragments.
Thousands of supporters of Mr. Morsi, who was sacked by the armed forces on Wednesday, had stormed Tahir square and other locations across the country on Friday demanding his reinstatement.
The army deployed troops around Cairo before crowds gathered outside the officers’ club of the Presidential Guard, where Mr Morsi is believed to be held.
The BBC said shots were fired as the crowd pushed towards the soldiers, first into the air, then into the crowds. One man in thirties with a beard fell to the ground, with blood on his clothes.
“One protester broke away from the rally to stick a pro-Morsi poster on the barbed-wire around the barracks. He was shot in the head with birdshot,” Aljazeera quoted its correspondent as saying.
Tens of thousands of protesters, mainly members of Muslim Brotherhood which Mr. Morsi belongs to, have also gathered in other parts of the country, vowing to continue until Mr. Morsi’s dramatic removal is reversed.
Reports quote a Senior Muslim Brotherhood member, Mohamed ElBeltagy, as urging demonstrators to go on to the Republican Guard as “martyrs in million”.
“Your brothers are now at the Republican Guards trying to help president Morsi get out. Your brothers are being fired at with live bullets.
“I call on the military is to remove the defence minister and to bring president Morsi back to power. We are going to the republican guards as martyrs in million. Today, president Morsi should come back to power,” Mr. ElBeltagy said.
The former president’s removal by the military after days of street protests by anti-Morsi Egyptians has sparked widespread anger from his supporters amid fears the move bears the potential of tipping the region’s most populous nation to severe crisis and even bloodshed.
The military’s decision has hardly been condemned by world powers including the United States as statements only express “concern” over the development. The U.S. has come short of describing the events as a military coup.
The crowds in Egypt are expected to swell further after Friday afternoon prayers in response to the call by a coalition of Islamist groups led by the Muslim Brotherhood for demonstrations against the coup.
Meanwhile, Egypt’s military has appealed for conciliation and warned against unrest, as police rounded up senior Islamists ahead of the planned Brotherhood protests on Friday.
The authorities have also closed the Rafah border crossing with Gaza for the day. Excessive protests, the army warned, could lead to civil unrest, while reiterating that it was not targeting any political group.