Scores of supporters of ousted Egyptian president Mohamed Morsi have been killed in clashes with security forces in the capital, Cairo, after a night of mass protests.

The exact death toll from Saturday's violence was not immediately clear, but Al Jazeera's Hoda Abdel Hamid, reporting from Cairo, says the health ministry has put the figure at 60 killed so far, based on the number of bodies recieved at the morgue, while doctors at the field hospital in Nasr City, where the pro-Morsi supporters have been gathering at the Rabaah al-Adawiyah Mosque for nearly a month, have put the number as high as 120.

Running battles broke out at dawn, with police firing tear gas at stone-throwing protesters, the official MENA news agency said.

If the death toll of 120 is confirmed it would be the deadliest incident since Morsi was deposed by the army more than three weeks ago.

On July 8, 53 people, mostly Morsi supporters, died when armed men opened fire close to a Republican Guard compound in the area.

Hundreds of people were wounded, medics said, warning that they could not cope with all the casualties.

The prosecutor-general's office announced on Saturday that it would launch an investigation into the violence.

In a press conference on Saturday, the interior minister, Mohamed Ibrahim, accused the Muslim Brotherhood of provoking the violence in order to win sympathy from the public.

He denied that the police used firearms against civilians, but said police were fired on by protesters. "Large numbers of officers suffered wounds as a result of live ammunition," he said.

Al Jazeera's Hoda Abdel Hamid, reporting from Cairo, said anti-military protesters still continued their sit-ins at different places on Saturday, while military supporters had gone home after demonstrations on Friday.

"The atmosphere is very, very tense, after a statement from the army said that it would have to tackle the 'issue'," she said. "It feels like the security forces eventually are going to storm pro-Morsi protests."

Supporters and opponents of Morsi staged mass rival rallies across the country on Friday, bringing hundreds of thousands into the streets and laying bare deep divisions within the Arab world's most populous country.

Army chief General Abdel Fattah al-Sisi had called for a mass show of support on Friday for a crackdown on what he called "terrorism".

Hundreds of thousands of anti-Morsi protesters obliged and gathered in Cairo's Tahrir Square and around the Itihadiya presidential palace.

'Shooting to kill'

Gehad El-Haddad, the Muslim Brotherhood spokesman, said the shooting started shortly before pre-dawn morning prayers on the fringes of the vigil being staged by backers of Morsi.

"They are not shooting to wound, they are shooting to kill," Haddad said.

Thousands of supporters and opponents of the army's removal of Morsi also took to the streets of the Mediterranean city of Alexandria, sparking fierce clashes that killed seven people and wounded 194.

A group of people who were trapped by armed men in one of the city's main mosques have been released, but 70 remain inside, including women and children.

The Brotherhood's political arm, the Freedom and Justice Party, called for more protests in the city.

European Union foreign policy chief Catherine Ashton has "deeply deplored" the deaths and urged all sides to halt violence, the EU said on Saturday.

The bloodshed came as the military-backed interior minister, Mohammed Ibrahim, warned a long-running sit-in in Cairo by Morsi loyalists would be ended "in the framework of the law".

There was little mention of the violence on Egypt's two state television channels, which broadcast weather reports and a talk show on Saturday morning.

Well over 200 people have died in violence since the overthrow of Morsi on July 3, most of them Brotherhood supporters.

The violence came after the authorities charged Morsi with murder and formally remanded him in custody for 15 days. He had been held without charge since hours after his ouster.

Morsi stands accused of the "premeditated murder of some prisoners, officers and soldiers" when he broke out of prison during the 2011 uprising that toppled veteran strongman Hosni Mubarak, MENA said.