Human Rights Watch has called upon Egyptian authorities to protect churches and religious institutions from mob attacks.

The organisation said at least 42 churches and dozens of Christian institutions had been attacked since August 14 across the governorates of Minya, Asyut, Fayum, Giza, Suez, Sohag, Bani Suef, and North Sinai.

In addition to being torched and damaged, many Christian properties have been looted. At least three Christians have died in the attacks, which were carried out after Muslim Brotherhood sit-ins in Cairo were violently broken up.

HRW is demanding an investigation into reports that security forces did nothing to prevent the attacks even when they had been made aware of the risk.

"For weeks, everyone could see these attacks coming, with Muslim Brotherhood members accusing Coptic Christians of a role in Mohammad Morsi's ouster, but the authorities did little or nothing to prevent them," said Joe Stork, acting Middle East director at Human Rights Watch.

"Now dozens of churches are smoldering ruins, and Christians throughout the country are hiding in their homes, afraid for their very lives."

As part of its own investigation into the situation, Human Rights Watch spoke with 43 witnesses, priests, and Coptic activists, who confirmed the attacks on 42 churches, dozens of Christian institutions and schools, and Coptic-owned businesses and homes.

It also visited 11 sites where attacks had taken place in Minya city and Bani Suef, and spoke to the head of the security directorate for Minya governorate.

In the vast majority of the 42 cases Human Rights Watch documented, police and the military were absent.

• In Dalga, a village in southern Minya governorate, residents said that men had attacked the local police station around the same time. Another Dalga resident said that on August 16 the governor promised to send armored personnel carriers to protect Copts from ongoing violence, but that none came.
• In Kirdassa, Giza, west of Cairo, an activist said that mobs attacked the local police station, killing 15 officers according to the Associated Press, before attacking Al-Mallak church.
• In Malawi, a town in Minya governorate south of Minya city, a priest told Human Rights Watch that he called emergency services and police multiple times while mobs burned his church, but no one came.

Coptic Bishop General of Minya Anba Makarios told Human Rights Watch that church officials had spoken to the prime minister, minister of interior, and a military official asking them to intervene. Despite promises of protection, no help came.

In one case, assistance arrived too late. A resident in Hadeyeq Helwan, 30 kilometres south of Cairo, told Human Rights Watch that one armoured personnel carrier arrived on the afternoon of August 17, a day after St George Church was attacked.

HRW also echoed previous reports of Coptic-owned buildings in Minya being marked with a black cross to single them out for attack.

Parts of the Muslim Brotherhood have accused Copts of conspiring in the removal of President Mohamed Morsi. In areas where churches were attacked, residents and clergy reported local religious leaders inciting groups to carry out the attacks.

A YouTube video of a pro-Morsi march on July 12 shows marchers chanting "Islamic Islamic despite the Christians" as they pass a church.

There have also been conflicting messages from the Brotherhood's Freedom and Justice Party. Its Helwan Branch posted a statement on the group's Facebook page accusing Pope Tawadros, the religious leader of the Egyptian Coptic community, of participating in Morsi's removal and of inciting Copts to block roads, encircle mosques, and storm them. The message ended with, "For every action there is a reaction."

However, two days later party spokesman Dr Mourad Ali said in a statement, "Pursuant to our party's indivisible principles, we strongly condemn any attack, even verbal, against Copts, their churches or their property."

On the same day, the Muslim Brotherhood website published a story with the headline, "The police and the church open fire on the al-Haram march at Giza tunnel and Murad Street."

Stork added: "While a few Muslim Brotherhood leaders have condemned these attacks, they also need to tell the group's followers to stop inciting violence by insinuating that the Coptic minority is responsible for the crackdown."

Watch Human Rights Watch's report into attacks on churches here: