The demonstration against the ruling Muslim Brotherhood left some members of the public angry at not being able to access services in Egypt's largest administration building, Ahram Online reported.
The situation was relatively calm Tuesday morning compared to late Monday when dozens of protesters were injured as security forces used birdshot, teargas and water to disperse the crowd.
Clashes intensified after midnight when an armored Central Security Forces vehicle reportedly drove toward protesters and was set on fire.
Hundreds of protesters in Cairo and other governorates took to the streets Monday to mark the second anniversary of the ouster of former President Hosni Mubarak.
Thirty-nine arrests were made across Egypt, the state news agency MENA reported.