Egypt’s military locked down the capital in response, blocking key entrances into Cairo and completely sealing off Tahrir Square to prevent anyone from entering what is considered the birthplace of the January 25, 2011 revolution that brought down the government of Hosni Mubarak.

The latest clashes came two days after the military and riot police cleared two pro-Brotherhood protest camps in one of the bloodiest days of Egypt’s modern history, leaving at least 638 people dead and more than 4200 injured.

In what the Muslim Brotherhood described as a “Friday of Rage”, marches left from 28 mosques around Cairo, aiming to meet in Ramses Square in Downtown.

With the country under a state of emergency and many provinces including Cairo hit by dusk until dawn curfews, the Interior Ministry ordered police to use live fire if government buildings came under attack.

Protesters reported that military helicopters were firing on people from the air, and a makeshift field hospital established in al-Fath Mosque just off Ramses Square was quickly overwhelmed with the dead and injured.

The air was filled with clouds of tear gas and smoke billowed from a building that had been set on fire, while helicopters hovered in the sky.

Huddling in a doorway of a nearby street as gunshots echoed around the buildings, 35-year-old Diaa Kassim said he witnessed civilians being shot from military helicopters hovering low over the large Brotherhood protests.

“There are also snipers in the buildings around here, many of them are wearing plain clothes but we know they are government supporters.”

“I am no Islamist,” said Mr Kassim, a clean-shaven customer service manager from the Imbaba neighbourhood in Cairo. “But I believe they need to return Mursi to the presidency. People here fear that Sisi has gone too far and that he will kill everybody in this fight.”

There were also reports of Muslim Brotherhood protesters firing back at police.

At the entrance to the May 15 Bridge there was almost constant gunfire, reportedly coming from Brotherhood protesters, while groups of local men, some armed with steel pipes and large machetes stood guard at the entrance to streets to prevent the protesters from entering.

“The Brotherhood are crazy,” one young man told Fairfax Media as people in the adjacent street ducked for cover as bullets whizzed by. “They are sniping from the bridge and attacking us.”

The protesters are calling for the reinstatement of Egypt's deposed president Mohamed Mursi, who has been held at an undisclosed location since the army stepped in – they say in response to millions-strong public protests – and removed him from office on July 3.

Rows and rows of armoured personnel carriers blocked roads around the capital as the clashes continued well into the late afternoon and marches continued to push towards Ramses Square along 6th of October Bridge from Nasr City.

There are now fears about how both protesters and the military will react as the deadline for tonight’s curfew approaches – like each day of the last six weeks of Egypt’s political crisis, neither side shows any signs of backing down.