CAIRO, Egypt — Hopes that the Egyptian revolution would lead to greater religious tolerance were jeopardized last week, after Muslims clashed with Christians who were protesting the arson of an Orthodox church.

According to media reports, a mob of rampaging Muslims killed six Christians and five Muslims in the violence, which took place in the Cairo suburb of Soul. At least 90 people were injured.

The attack occurred shortly after Egypt’s new leader, Prime Minister Essam Sharaf, met with Coptic leaders to reassure them of his commitment to religious equality.

Thousands of Christians held a sit-in in front of the Television Building in central Cairo, blocking traffic in a major thoroughfare. On Tuesday night, more than 2,000 Christians took their protest to a central highway, burning tires and pelting cars with rocks, The Associated Press reported. The dead were killed in the ensuing clashes.

The March 5 arson attack in Soul — the first major anti-Christian incident since the popular uprising that toppled the regime of Egyptian President Hosni Mubarak — destroyed the Church of St. Mina and St. George in Soul, which is home to 6,000 Christians and thousands of Muslims.

An estimated 4,000 Muslims attacked Coptic homes and set fire to the church, which was destroyed. Muslims have since put up signs saying the church’s property will be used to erect a mosque. Threatened with death, many Christians fled to neighboring villages.

At the time, church officials hoped the meeting with Sharaf — believed to be the first time an Egyptian leader has spoken with street protesters — could be the first sign since the popular revolution that religious tolerance could become a national priority.

Speaking by phone from Cairo, Coptic Catholic Patriarch Antonios Naguib of Alexandria called the meeting, which was attended by the Orthodox Coptic leadership, a positive sign.

“I was afraid there would be no [government] action to deal with the situation, but when I saw this intervention, and the decision to rebuild the church and to allow the people back into their homes, it gave me hope,” Cardinal Naguib said.

Ihab Aziz, executive director of the Coptic American Friendship Association, said Christian representatives had won several important concessions from the prime minister.

He promised to rebuild the church, despite pleas from local Muslims that it be rebuilt outside the village. He promised to use military police to secure the safety of Christians inside the village and to allow the many Christians, mostly women and children who fled, to return.

The representatives also requested the release of Metias Wahba, whom, according to Aziz, the government imprisoned for performing a marriage between a Copt and a Muslim who converted to Christianity.

This is not a punishable crime according to the law, Aziz said.

Eyewitnesses told the Assyrian International News Agency (AINA) that the Muslim attackers were angered by a romantic relationship between a Coptic man and a Muslim woman. They said the mob prevented firefighters from entering the village.

Quoting the officer in charge, AINA said that the army, which had been stationed in the village next to Soul, initially refused to enter the village. When the army finally sent three tanks to the village, Muslim elders sent them away, saying that everything was already in order.

Aziz said the mob was evidently incited to violence during a joint funeral for the Muslim woman’s father and cousin. The woman’s male cousin murdered her father because he refused to murder her for undermining the family’s honor. The woman’s brother murdered the cousin to avenge his father’s death.

Aziz said Muslims burst into the church and stole everything, including the offering boxes. He said 1,500 of the most vulnerable Christians left, while the men stayed to defend their homes.

Christians in other parts of the Middle East are also facing uncertainty, according to Bishop Paul Hinder, the apostolic vicar to Arabia.

Bishop Hinder, whose diocese includes Qatar, Bahrain, Yemen, Saudi Arabia and the United Arab Emirates, emphasized that the turmoil in Bahrain and Yemen has not been targeted specifically toward Christians.

During the initial unrest in Bahrain, Bishop Hinder said, local Church officials decided to cancel Mass due to a curfew. An estimated 60,000 to 80,000 Catholics call Bahrain home, he said.

“Already, by last week, things were almost back to normal. I’ve been in touch with the parish priest, and he’s said there are no major problems. Of course, things can change in a short time,” the bishop said.

Bishop Hinder said members of Yemen’s tiny Christian minority (about 3,000 in a country of 20 million people) have been unable to reach Church institutions not because they are Christian, but because of general difficulties in the country right now.

In Tunisia, Bishop Lahham Maroun called the Catholic Church a “foreign entity” because Christians there are foreigners.

“We were not actors to what’s been happening here, and the life of the Church, our work, has not changed.”

Michele Chabin writes from Jerusalem.