The secretariat complex is a few metres from the National Assembly and the Presidential Villa.
The youths, who were armed with stones, chased away a police team and overturned a traffic warden cabin on the road.
They also reportedly injured the Federal Secretariat Divisional Police Crime officer in the face after he asked them to stop harassing motorists.
Chanting “Free El-Zakyzaky,” the Shiite members dared the Police to engage and dislodge them.
A team of policemen has just arrived to dislodge the angry youths.