Prime Minister Kamal Ganzouri accused the demonstrators of mounting "an attack against the revolution."
Al Jazeera's reports did not say that the protesters had attacked the soldiers, and ascribed the violence only to the army. They added that the military had burned down protesters' tents.
The sit-in began three weeks ago after the appointment of Ganzouri by Egypt's governing military council. The protesters want the generals to transfer power immediately to a civilian authority, and not wait until a presidential election in mid-2012.
Protesters threw stones at the soldiers, who responded with stones and baton charges. Plainclothes and uniformed security officers threw rocks at the activists from the roof of the parliament building. Some in the crowd threw fire bombs, causing part of the building and several cars to catch fire.