The arrests took place on Thursday evening near Nar region in northern Cairo as the clashes erupted between the security forces and extremist groups, Al-Alam reported.
The security forces fired tear gas to disperse the hardline Islamist protesters who were attempting to break the entrance door of the security center.
At the height of the protest, no police presence was visible outside the security headquarters, where protesters tore down Interior Ministry flags and erected several al Qaeda flags and set off fireworks.
Around 2,000 protesters from several Salafi groups staged the protest and called for release some their leaders who were arrested earlier.
Earlier on Thursday, an Egyptian judge referred a complaint filed by a police spokesman against a hardline cleric Hazem Salah Abu Ismail to the state security prosecution, setting a hearing for Saturday to begin the investigation.
State newspaper Al-Ahram reported that the complaint called for Interior Minister Mohamed Ibrahim to arrest Abu Ismail on charges of "terrorising police officers" after Abu Ismail urged his supporters to attend Thursday's protest.
This is while April 6 movement also called on its supporters to take to the streets on Friday to surround the national security headquarter in a bid to join other extremist groups.