A deadly shooting at the site of a sit-in by Muslim Brotherhood supporters in Cairo, demanding the reinstatement of ousted President Mohamed Morsi, has left dozens of people dead.

The Egyptian health ministry said at least 51 people had been killed and more than 300 injured in the incident early on Monday morning.

Egypt's interim administration has expressed "deep regret" for those killed in violence in Cairo on Monday, it said in a statement carried on the state news agency.

The transitional administration also said it had formed a judicial committee to investigate the events. The statement called on protesters not to approach any military or "other vital installations".

Mohamed Mohamed Ibrahim El-Beltagy, a Brotherhood MP, described the incident during dawn prayers after police had stormed the site, as a "massacre".

About 500 people were also reportedly injured.

A doctor told Al Jazeera that "the majority of injured had gunshot wounds to the head".

The Brotherhood said the dead and the injured have been taken to a makeshift hospital in the the Nasr City neighbourhood.

Speaking to Al Jazeera, Gehad Haddad, a spokesman for Muslim Brotherhood, said that at around 3.30 in the morning, army and police forces started firing at sit-in protesters in front of the Republican Guard headquarters in Cairo.

“We have people hit in the head, we have bullets that exploded as they entered the body, cluttering organs and body parts” said Haddad.

“Every police force in the world understands how to disperse a sit-in. This is just a criminal activity targeting protesters.”

However, the military, which has set up checkpoints around Nasr City, said a "terrorist group" was responsible, adding that two officer had also been killed.

In a press conference held in Cairo on Monday, Hany Abdel Latif, Egypt's interior ministry spokesman, said that "the Egyptian police is the force of the people. They are operating for all the Egyptian people, with all their affiliations."

"The Egyptian security forces are working to safeguard the freedom of the Egyptian people following the January 2011 revolution," said Abdel Latif, adding that the police and security apparatus will not protect any particular regime, not "the former, the existing, or the upcoming".

"The Egyptian police is out of the political equation. It can not be part of any political process in any way, shape or form," said Abdel Latif.

Speaking at the same press conference, military spokesman Ahmed Ali blamed the violence on protesters who attacked the Republican Guard headquarters and defended the actions of the security forces, saying that the acted in self-defence against armed men attacking them from various locations, including rooftops.

Ongoing violence

Dozens have died and more than 1,000 people have been injured in street clashes between supporters and opponents of Morsi in the aftermath of the military coup on Wednesday.

Also on Monday, Egypt closed down the Cairo headquarters of the Muslim Brotherhood, saying weapons were found inside it.

The latest violence further raised political tensions, even as the country's interim leadership struggled to find a consensus on who should be the prime minister.

The Salafist Nour Party announced it was suspending its participation from talks over new government in protest against Monday's fatal shootings.

Earlier reports said interim president Adly Mansour was leaning toward appointing centre-left lawyer Ziad Bahaa Eldin as prime minister after members of the Nour Party expressed concern at an earlier suggestion that the job could go to Nobel Laureate Mohamed ElBaradei.

But some Nour Party members expressed concern that the candidates had political affiliations.

Younes Makhyoun, Nour's leader, told Reuters news agency: "Both are from the same party, the National Salvation Front, this is rejected. I fear it would be going from one exclusive approach to another," referring to accusations that the Brotherhood tried to monopolise power.

Meanwhile, popular Salafist preacher Yaser Borhamy told Al Jazeera that he has nothing against Bahaa eldin, but that he "would rather have someone who does not belong to a political party - a pure technocrat if such thing exists," said Al Jazeera's Hoda Abdel-Hamid.

She said others from Nour had been seen on local media channels saying they approve of Bahaa Eldin.

AFP reported that the prime minister would be named on Monday, quoting the interim president's adviser.

Nour has agreed to the the army's roadmap for the political transition, giving the military Islamist support for an overthrow rejected by Islamist parties aligned wtih Morsi's Muslim Brotherhood.

Unlike Nour, the Muslim Brotherhood has said it would have no part in the military-backed political process.

The army has denied it staged a coup, saying instead it was merely enforcing the will of the people after mass protests on June 30 calling for Morsi's resignation.

The pro-Morsi camp is refusing to budge until its leader is restored, and Egyptian state TV reports that some of the 200 supporters of Morsi arrested earlier on Monday have been released.