Egyptian soldiers and demonstrators engaged in stone-throwing battles in downtown Cairo on Saturday, the second day of a brutal crackdown on anti-government protests that has left at least nine dead and hundreds more injured.

Early in the day, security forces who had sealed off nearby streets came under a barrage of stones thrown by hundreds of demonstrators. Later, soldiers took to nearby rooftops where they hurled stones and bricks at the crowds in the streets below.

Other soldiers armed with batons and sticks and dressed in riot gear chased protesters through Tahrir Square, smashing TV cameras as they went. Images from the scene appeared to show soldiers beating unarmed protesters as they placed them under arrest.

In the background, a massive plume of black smoke rose from a two-story building that had been set on fire.

The soldiers then set fire to tents in the square that famously served as the epicentre of the ‘Arab Spring' uprising that toppled former president Hosni Mubarak in February.

The violence was in stark contrast to this week's peaceful conclusion of the second round of voting in parliamentary elections. Many have described the elections as the fairest vote in the country's modern history.

But protesters are now demanding the ruling military council yield authority immediately to civilians. Similar clashes between demonstrators and the military in November left more than 40 people dead.

The state-run news agency MENA said at least eight people have been killed and about 300 people injured in two days of clashes.

Prime Minister Kamal Ganzouri said some people had died from gunshot wounds but he denied that security forces had anything to do with the deaths. He said a group had fired at the protesters from behind.

"I feel very sad and in so much pain," he said on state TV. "I stress here that the armed forces didn't engage with protesters and didn't leave the building."

But rights groups and activists claim the military is merely emulating the practices of the Mubarak regime by arresting and beating dissidents.

The latest violence erupted late Thursday after soldiers stormed a protest camp outside the cabinet building near Tahrir Square. Witnesses said troops took a protester into the parliament building where they beat him.

Among those killed Friday was Sheik Emad Effat, a cleric from Al-Azhar, Egypt's most eminent religious institution. Effat, who had been criticizing the military, was shot in the chest after joining the protesters outside the cabinet building.

In a statement Friday night, the ruling military said its officers showed self-restraint but denied they had used any gunfire. It said the clashes began when a military officer was attacked while on duty and protesters tried to break into the parliament compound.

With files from The Associated Press