Egypt's interim leader has expressed sorrow over the deaths of at least 51 people near a barracks in Cairo, urging restraint amid ongoing unrest.
Adly Mansour also said he had ordered an investigation into the deaths.
The Muslim Brotherhood says its members were fired on as they staged a sit-in for ousted President Mohammad Morsi, while the army said it had responded to an armed provocation.
The Brotherhood's political wing meanwhile called for an "uprising".
The Freedom and Justice Party (FJP) - which took nearly half the seats in historic parliamentary elections held in late 2011 and early 2012 - urged Egyptians to revolt against "those trying to steal their revolution with tanks".
Tens of thousands of Mr Morsi's supporters have gathered at their traditional rallying place, near Cairo's Rabaa al-Adawiya mosque, for a third day of protests.It also urged the international community to intervene to "stop further massacres" and prevent Egypt becoming "a new Syria". The movement has accused the army of staging a coup.
Mr Morsi, an Islamist and Egypt's first freely elected leader, was ousted by the army last week after mass protests.
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".
The killings follow an incident in the same location on Friday in which three people died and dozens were wounded as troops fired on crowds.
Mr Morsi is believed by the Muslim Brotherhood to be held at the barracks, but the military says he is elsewhere.
In a separate development, the grand sheikh of al-Azhar University, Ahmed al-Tayeb - seen as the highest authority in Sunni Islam - warned of civil war and said he was going into seclusion until the violence was over.
In a statement read out on state TV, Mr Mansour's office expressed "deep sorrow" over the deaths in the "painful incidents" on Monday morning.
He urged self-restraint to uphold national interests and the country's security, adding that a judicial committee would investigate the deaths and announce its results to the public.
He gave the army's version of events, describing the incident as an attempt to storm the Presidential Guard barracks.
Mr Mansour urged protesters not to approach the military or "vital installations".
Meanwhile the United States condemned the violence in Egypt and called for "maximum restraint" after the killings.
A White House statement said Washington was "not aligned" with any political movement, adding that cutting military aid to Egypt was not in US interests.
'Guns and tear gas'There were conflicting reports over what happened outside the barracks 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.
Later, in an emotional news briefing, members of the Brotherhood said military chief Gen Abdul Fattah al-Sisi was "an assassin and a butcher".
The health ministry said at least 51 people were killed and 435 people wounded.
Speaking to journalists, army spokesman Col Ahmed Mohammed Ali said a group armed with live ammunition, petrol bombs and stones had attacked security forces.
He said that two police and one soldier were killed in the exchange of fire. Eight soldiers were critically wounded.
The spokesman added that one soldier had been shot through the top of the head from above, indicating that snipers were firing from high buildings.
Col Ali also disputed claims that children had died, saying pictures of dead children posted on the internet were in fact images taken in Syria in March.
The BBC's Lyse Doucet in Cairo says that while both sides have video which they say proves that they are right; what matters now is what people believe happened.
Col Ali said that the army was not taking sides and peaceful demonstrators had nothing to fear.
"The angry protester is a brother to all Egyptians, and so long as he remains peaceful it is the responsibility of the armed forces to protect him," he said.
Mr Morsi was ousted on Wednesday by the military. It said it was responding to the demands of anti-Morsi protesters across Egypt, 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 - who has pledged to hold elections, although no date has yet been given.
The army has insisted it does not want to remain in power.
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.
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