At least 52 churches were targeted in a 24-hour span starting Wednesday, at the same time as the violence exploded in Cairo between supporters of Morsi and the Muslim Brotherhood and the secular military, said Bishop Angaelos, the Cairo-born head of the Coptic Orthodox Church in the U.K.
Ishak Ibrahim said his organization, the Egyptian Initiative for Personal Rights, has confirmed attacks on at least 30 churches, as well as related facilities including schools.
Witnesses described a mob attacking the Virgin Mary Church in Giza, chanting for Egypt to become an "Islamic state" and looting the 67-year-old building.
The attacks have been blamed on supporters of the Muslim Brotherhood, but amid the chaos in the capital, the perpetrators may remain unidentified for some time.
The United Nations condemned the attacks noting that "a number of Christian churches and institutions have been targeted, including in the provinces of Assiut, Fayoum, Minya and Sohag, reportedly in retaliation to the incidents in Cairo."
"We urge all Egyptians to act responsibly during these difficult moments and refrain from using violence to express their grievances, in particular by targeting religious minorities and institutions, or by using language and inciting behaviors that may escalate tensions," said UN special adviser on the prevention of genocide Adama Dieng. "We call all political and social actors to abandon strategies of confrontation."
But Angaelos and Coptic Pope Tawadros II, anticipating the violence might turn against Copts, issued a warning and suspended public events.
Sectarian violence has risen since the ouster of President Hosni Mubarak, in 2011, with clashes breaking out as recently as April around Egypt's largest cathedral.
"In the past two-and-a-half years, we've had more deaths of people just because they are Christians than in the last 20 years," Angaelos said.
And the Islamist Brotherhood has not shied away from expressing its dislike of the Christian sect -- but deny the division is religiously motivated.
"I don't dislike them as a sect or as a people. To the contrary," a senior Brotherhood figure said. "Our concern is that they have blindly backed a military and an old guard who has seized from us our legitimate rights. Were this to have happened to them, they would have been the loudest to complain."
Recent estimates put the number of Copts in Egypt at 9 percent of the country's population of 85 million.
More than 600 people have been killed in the clashes since Wednesday in Cairo as the Muslim Brotherhood called for a "Friday of Rage" and the military-led government cracked down on the protesters.