Barbed wire blocked roads into Tahrir Square, the epicentre of the protests that toppled President Hosni Mubarak on February 11.
Protesters cried “revolution, revolution” and brandished an effigy of Field Marshal Mohamed Hussein Tantawi, who heads the military council now ruling Egypt and is also defence minister.
“What is wanted is a civilian council,” read one slogan. Another said: “Topple the Minister of Defence.”
Medical sources said 13 men were wounded by gunfire and two had died on Friday night during the biggest rally since February 18, when millions turned out across Egypt to celebrate Mubarak’s downfall.
In scenes reminiscent of the protests that brought down Mubarak, soldiers and police used tasers and batons to try to drive the protesters out of Tahrir.
After failing to remove all of them, the army backed out of the square.
There was little security presence in the square on Sunday morning. A burnt out vehicle crouched as a reminder of the violence and men were sweeping rubbish into piles.