As hundreds of Islamists were being gunned down on the streets of Cairo during Wednesday’s bloodbath, the ugly consequences began to ripple hundreds of miles down river to the towns and cities along Egypt’s Nile Valley.

Outraged supporters of toppled President Mohamed Morsi, reacting to the ferocious crackdown launched against protesters camped out in Cairo, started attacking police stations and government institutions in several provinces. Scores were killed and many more wounded. But in a development which does not bode well for an already fractured society, it was the nation’s Coptics which bore the brunt of some of the worst violence.

Christians account for an estimated 10 per cent of the country’s 85 million population. A former Coptic Pope, Kyrillos VI, once claimed that Egypt’s Muslims and Christians were a single people “ worshipping the same God in two different ways.”

Download the new Independent Premium app Sharing the full story, not just the headlines

Yet following Wednesday’s nationwide violence, when churches, Christian-owned businesses and property were attacked by angry mobs, Egypt’s Copts appear to be feeling increasingly vulnerable.

“I’m expecting a period of heavy assaults against Christians,” said Kamel Saleh, a member of the Coptic church’s senior lay committee. Mr Saleh added that ever since 30 June, when huge crowds of protesters began calling for the resignation of Mohamed Morsi, church leaders had been engaged in contingency planning to decide how Christians could respond to expected attacks. “The churches themselves are just buildings and can be repaired,” said Mr Saleh. “ What worries me is the unprecedented level of violence which will be difficult to climb down from.”

Following the decision by Pope Tawadros, the Coptic Patriarch, to give his blessing to the 3 July coup, officials were expecting the worst. But inflammatory speeches from Cairo’s tent encampments were enough to convince some Christians that Islamists harboured violent intentions. Safwat Hegazy was among those who spoke to pro-Morsi protesters during the Cairo sit-ins. Hegazy, a television imam, has made fiery declamations “There is no doubt in my mind that the Muslim Brotherhood are able to influence the violent groups who attacked Christians,” Mr Saleh said.

According to Ishak Ibrahim, a Cairo-based human rights researcher focusing on religious issues, a total of 23 churches across the country were torched by angry mobs following Wednesday’s operation by the security services. At least seven were completely destroyed, he said. Two monasteries were also attacked.

In the city of Sohag, the Bishop of Mar Girgis Church reported that the building had been set alight by supporters of the Muslim Brotherhood. There were no police present – a common feature in many of the attacks, according to witnesses.

Mr Ibrahim said the recent violence has the potential to become much more serious. “It will become a big problem,” he said.

Video: Travellers can still go to Red Sea resorts