Samir Iskander and his son, and Nasim Farouk Awad, who are Christians, turned themselves in out of fear they would face assaults, the Cairo newspaper al-Masry al-Youm reported.
Seven were killed April 5 in clashes after young children allegedly painted swastikas on the walls of an Islamic church in Khosous, and during their funerals in Cairo, two others were killed and tear gas was fired into the Coptic Cathedral, the newspaper said.
Police said they had earlier arrested two brothers of the same family on charges of participating in the April 5 incidents.
Investigators said the brothers sparked the violence when they fired at Muslims protesting near their home, adjacent to the school, killing one Muslim and wounding two others.
2014: The Year in Music [PHOTOS]