Twenty-eight people were arrested on suspicion of attacking soldiers and burning military vehicles during clashes between the army and demonstrators, state media reported on Tuesday.
At least 25 people were killed when troops broke up protests near Cairo's state television building (Maspero) on Sunday night, in the worst violence seen since former president Hosni Mubarak was overthrown in February.
The demonstrators, mostly Coptic Christians who were later joined by some Muslims, were protesting against an attack on a church in the southern city of Aswan last week.
Politicians from all sides have accused Egypt's ruling military council of mishandling the protests.
The council's failure to give a clear timetable for handing power to civilians has also stroked tensions, say commentators.
The 28 suspects, who included Christians and Muslims, will be detained for 15 days pending investigations, state news agency MENA said.
The suspects were detained on suspicion of participating in acts of vandalism, attacks on members of the armed forces, and burning of army property, MENA quoted an official as saying.
The investigation of the civilian suspects in these events falls within the jurisdiction of the military courts in light of encroachments on the armed forces and its elements that were present in Maspero, the official added.