The prisoners were killed after taking a police officer hostage while being transferred in a police vehicle to Abu Zaabal prison near Cairo, Al-Jazeera news reported.
It said the men had been arrested in the clear out of Cairo's Al-Fateh mosque yesterday.
However, the state-run MENA news agency reported that "unknown gunmen" had tried to aid the prisoners.
The gunmen exchanged fire with guards of the trucks carrying over 600 people detained in street violence between security forces and supporters of ousted President Mohammed Morsi, the agency said.
It described the detainees and the gunmen as belonging to the Muslim Brotherhood.