They were held when rumours of a new church being built sparked the looting of a Christian community centre near the Mediterranean port of Alexandria.
Naeem Aziz, the owner of the building in the village of Qarayat al Bayda, said the building under construction was actually going to be a house for his son.
Nevertheless, the property, its building materials and nearby homes were attacked and looted by a large crowd chanting "we don't want a church."
The community centre belonged to the local Church of the Holy Virgin and the Archangel Michael, while a car belonging to the priest, Father Karass, was damaged.
A nearby motorcycle was set on fire.
Ramy Kashwaa, a local Coptic activist who witnessed the events first-hand stated: "Had it not been for the intervention of our sane Muslim brothers, the pastor could have died."
Six Muslims were arrested were freed shortly afterwards, however, the six Copts were not released until dawn on Saturday and they have now been charged with holding prayers without permission and building without permit.
Mr Aziz and his brother Moussa were assaulted before being among six people detained by police who "allowed the destruction, violence and looting to continue", according to Christian Solidarity Worldwide.
CSW's Egypt Advocacy Officer, David (which is not his real name), told Premier: "In Egypt, no new church can be built without any other method than presidential decree.
"So that's one of the things we're following at the minute, and pressing the new Parliament in Egypt for.
"Christians are regularly facing acts of violence towards them, churches are being destroyed or looted or damaged, and then they subsequently can't build them again without the presidential decree."
Mervyn Thomas, Chief Executive of Christian Solidarity Worldwide (CSW), said: "We are concerned at the failure of the security services to ensure the safety of the Coptic Community and at the arrest of six Copts on spurious charges.
"We urge the Egyptian Government to ensure that security officers nationwide provide equal and adequate service to every community, regardless of religion.
"The security officers who failed to apprehend the aggressors and provide adequate protection to the Coptic Community should be prosecuted alongside with the perpetrators of these crimes. "