"The latest unrest in Cairo is a systematized plan to strike at the nation's security," a Supreme Council of the Armed Forces representative said at a news conference Monday, Ahram Online reported.
"Using violence against protesters is a fake allegation circulated by mass media," he said.
"If rioters target the buildings housing the People's Assembly, the Interior Ministry and the Cabinet offices, then it is clear that they know what they are doing and that they follow a specific agenda."
Troops and protesters clashed for a fourth day near the Egyptian Parliament, with two more fatalities reported by a doctor, Ahmed Khalil, raising the death toll to at least 13 since Friday.
Soldiers and police brandishing batons and tear gas entered Tahrir Square and chased people away but hours later the protesters returned, the BBC reported.
Hundreds of protesters threw rocks and firebombs. Security forces, on the ground and on rooftops, retaliated with rocks and water hoses, independent TV and amateur video indicated.
An activist accused the army and police of firing indiscriminately at protesters.
"They stormed into the square destroying cars, shops and the field clinic and they will blame it on the protesters," Gigi Ibrahim told CNN.
U.N. Secretary-General Ban Ki-moon said through a spokesman Sunday he was "highly alarmed by the excessive use of force employed by the security forces against protesters."