The Egyptian army has set up barricades outside the presidential palace, after ordering protesters to leave the area.
It follows violent overnight clashes between supporters and opponents of President Mohammed Morsi that left five people dead and 644 injured.
Most protesters left the palace by the 15:00 (13:00 GMT) deadline, though some opposition activists remained.
Meanwhile, Egypt's top Islamic body has called on the president to suspend his decree claiming sweeping powers.
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