The rival groups are supporters and opponents of President Mohammed Morsi.
The clashes followed two weeks of sporadic violence around the country since President Morsi, a former leader of the Muslim Brotherhood movement, seized temporary powers beyond the review of any court, removing the last check on his authority until ratification of the new constitution.
Egyptian military deployment was witnessed around the presidential palace and aims to secure the building, the state news agency reported on Thursday.
“The Republican Guard began a deployment around the headquarters of the presidency … to secure the headquarters of the presidency in its capacity as a symbol of the state and the official headquarters of government,” the agency reported.
The situation was calm Thursday morning, with thousands of Morsi supporters camping outside the palace after driving away opposition activists who had been staging a sit-in there.