At least 42 people have been shot dead near a military barracks in Cairo, amid ongoing unrest following the removal of Egypt's President Mohammed Morsi.
The Muslim Brotherhood says its members were staging a pro-Morsi sit-in at the barracks, where he is believed to be in detention, when they were fired on.
But the army said a "terrorist group" had tried to storm the barracks.
The office of interim president Adly Mansour expressed "deep sorrow" over the deaths and called for restraint.
In a statement, he too said there had been an attempt to storm the Presidential Guard barracks.
Mr Mansour ordered the formation of a judicial committee to investigate the clashes, and urged protesters not to approach the military or "vital installations".
The Freedom and Justice Party (FJP), the Brotherhood's political wing - which took nearly half the seats in historic parliamentary elections held in late 2011 and early 2012 - called on Egyptians to stage an "uprising" against "those trying to steal their revolution with tanks".
It also urged the international community to intervene to "stop further massacres" and prevent Egypt becoming "a new Syria".
The hardline Salafist Nour party - which had supported Mr Morsi's removal - said it was withdrawing from talks to choose an interim prime minister, describing the shooting incident as a "massacre".
Mr Morsi, an Islamist and Egypt's first freely elected leader, was ousted by the army last week after mass protests.
Scores of people have been killed since the unrest began at the end of last month.
Mr Morsi's supporters - many of them members of his Muslim Brotherhood movement - have been staging a sit-in outside the barracks, accusing the army of mounting a coup.
There were conflicting reports over what happened there on Monday morning.
The Brotherhood put the number of dead at 53, and said children were among the victims.
It said the army raided its sit-in at about 04:00 (02:00 GMT) as protesters were performing dawn prayers.
"We found the army, around a thousand army troops surrounding us and firing guns, and on the other side of the street the riot police firing tear gas," protester Mohamed Hassan told the Associated Press.
"They are pointing at our heads and chests. I saw with my own eyes 10 martyrs."
Later, in an emotional news briefing, members of the Brotherhood said military chief Gen Abdul Fattah al-Sisi was "an assassin and a butcher".
But the health ministry said at least 42 people were killed and some 300 people wounded.
In a statement read on state media, the army said "an armed terrorist group" had tried to storm the barracks.
An army officer was among those killed and a number of other soldiers were wounded, some critically, it said.
One soldier, Mohammed Ibrahim, told state TV from hospital that troops had been at the protest "to ensure the safety of the people".
"They started firing at us and throwing Molotov cocktails and bricks," he said.
"I was standing in the middle trying to calm things down and someone came and stabbed me with a piece of metal."
State TV showed footage of what it said were protesters shooting at soldiers.
The army's statement also said some 200 people had been arrested and were found to have weapons, ammunition and petrol bombs.
Prosecutors have also ordered the closure of the FJP headquarters in Cairo, after police said weapons were found inside.
Mr Morsi was ousted on Wednesday by the military. It said it was responding to the demands of the protesters, who accused him of becoming authoritarian and failing to tackle the economy.
He was replaced on Thursday by Adly Mansour - the head of the Supreme Constitutional Court. He has pledged to hold elections, but as yet no date has been given.
The army has insisted it does not want to remain in power.
On Sunday, tens of thousands of both supporters and opponents of Mr Morsi rallied in many Egyptian cities.
The BBC's Jim Muir in Cairo says the latest violence has derailed efforts to find a political way out of Egypt's crisis, leaving the country in a dire state.
The withdrawal of the ultra-conservative Nour party from the political transition talks will also set back efforts to appoint a new prime minister, our correspondent adds.
Though the Islamist party had backed the army-led "roadmap" to new elections, it had blocked the appointment of two potential prime ministers because of concerns over the shape of a new constitution.
One of those rejected by Nour, leading opposition figure Mohamed ElBaradei, condemned the violence and called for an "immediate independent and transparent investigation", saying Egypt was "in dire need of reconciliation".