Hundreds of protesters gathered Saturday at the state security services building in south-western Cairo, after they saw black smoke coming out of the building, dpa reported.
Witnesses told the German Press Agency dpa that protesters believe security officers are trying to burn documents inside the building, located in Sheikh Zayed neighbourhood.
Protesters demanded that the military, running the country in the wake of president Hosny Mubarak's ouster, suspend the security service.
The fire comes after a similar protest took place at the headquarters of the service in the northern coastal city of Alexandria.
Clashes erupted when officers fired shots in the air to disperse protesters late on Friday.
Videos posted on the internet showed Molotov cocktails being thrown from the building, and several cars parked nearby destroyed.
When protesters managed to enter the building they found documents cut and shredded inside the offices, fuelling suspicions that the security officers were trying to destroy incriminating evidence.
Demonstrations were held in both Alexandria and the capital Cairo on Friday, as people called on the military to dissolve the controversial State Security Investigations Service.
The service has been blamed for much of the violence against protesters that left more than 350 people dead in the popular uprising earlier this year.