Several members of the former regime are under investigation for ordering attacks on protesters during the height of the Egyptian revolution early this year.
Protesters have taken to the country's main square in Cairo since Mubarak fell. Christians in Cairo held a protest vigil near the city's Tahrir Square last week, demonstrating against attacks on two churches in which a dozen people died.
Government officials said the violence began over reports that a Christian woman married to a Muslim was being held against her will in the St. Mena Coptic Orthodox Church.
The ruling military council denied allegations that armed forces used live ammunition to break up any protests.
"The armed forces didn't and will not use force against the revolution's youth or any one of these great people," the council was quoted by Egyptian daily al-Masry al-Youm as saying.
The council dismissed the allegations as part of an effort to create divisions in the country.
Egypt is preparing for parliamentary and presidential elections later this year in order to replace the Mubarak and military governments.