Christian Solidarity Worldwide reports that at least 60 churches have been targeted by Islamists since the ousting of President Mohamed Morsi.
In some areas, like Minya, Beni Suef, Fayoum and Assiut, leaflets have been left at Christian homes and businesses warning them to leave or else face reprisals.
There are reports that Christian homes and businesses in Minya have been marked with black crosses to single them out for attack.
The Associated Press reported an attack on a Franciscan school in Beni Suef during which three nuns were paraded "like war prisoners" and two other female employees were sexually harassed and abused. The attackers also looted the property.
Services have been cancelled at churches caught up in the waves of violent protest across Egypt. Some churches were unable to go ahead with services because of the damage done to their buildings. Others cancelled services because of fear of attack.
The Egypt Independent reports that the unrest prompted the Virgin Mary and Priest Ibram monastery in Degla, south of Minya, to cancel prayers on Sunday for the first time in 1,600 years.
The violence has left around 830 people dead, including 70 policemen. CSW said at least seven Christians had been killed.
Christians are finding themselves on the receiving end of accusations from Islamists who say they colluded in the ousting of Morsi. The accusations have prompted some calls for retaliatory attacks.
CSW spokesperson Kiri Kankhwende condemned the spread of disinformation about the involvement of Christians.
She called upon the interim government to take steps to ensure the safety of all Egyptians.
"The sectarian targeting of the Coptic community by Morsi supporters, in misplaced retaliation for the actions of the army, cannot be divorced from the continuing campaign of defamation and disinformation emanating from key Brotherhood figures regarding the Church's role in Morsi's ousting," she said.
"Both the violence and the disinformation that fuels it are unacceptable and should be condemned in the strongest terms.
"While it is deeply encouraging to hear of moderate Muslims coming to the assistance of their Christian neighbours, the responsibility to protect lies ultimately with the Egyptian authorities.
"We therefore renew our call for the interim government to ensure comprehensive security to all Egyptians, and also urge and pray for peace and reconciliation."