The protesters, including members of the Black Bloc group, began demonstrating outside the offices of the prosecutor general and set fire to the entrance to the building, before heading to Tahrir Square and blocking traffic on the Qasr al-Nil bridge.
Satellite television station ONTV aired live footage showing security forces clashing with demonstrators on the Qasr al-Nil bridge.
Egypt's prosecutor general had ordered the arrest of several members of the Black Bloc, a violent group opposed to the Muslim Brotherhood and Islamist President Mohammed Mursi.
They present themselves as the defenders of protesters opposed to President Morsi's rule.
On their Facebook page, the activists say they are a "generation born of the blood of the martyrs" from the 2011 revolution that toppled former president Hosni Mubarak.
Prosecutor general Talaat Abdallah accused the group of "terrorism" three months ago.
