The militants have expelled 90 percent of Christians in Homs, which has faced the brunt of violence related to the uprising, and grabbed their homes, it said. They went door to door in the neighborhoods of Hamidiya and Bustan al-Diwan forcing Christians to flee without giving them the chance to take their belongings, it added.
Syria has witnessed protests against the government as part of the wider Arab Spring since last January.
About 10 percent of Syria's 23 million people are estimated to be Christians, who have generally supported President Bashar Assad, a Muslim from a Shiite offshoot who is autocratic but protects religious minorities. On the other hand, the majority of the Muslims in Syria are Sunni.
Homs had a large population of Christians, and Muslims from the Alawite sect to which the president belongs.
On the local Islamist group's association with al-Qaida and militants from Libya and Iraq, Giuseppe Nazzaro, the Vicar Apostolic of Syria's largest city of Aleppo, was quoted as saying, "We have no sources to confirm this information directly, but we can say that these relationships are beginning to break down the wall of silence built up to now by the press worldwide. In this situation Islamist and terrorist movements are making headway."
The Christian minority is being targeted in other cities as well. Last Sunday, the Vicar recalled, a car bomb exploded in the vicinity of the school of the Franciscan fathers in Aleppo. "By a miracle a massacre of children was avoided, at the Center of catechesis of the Church of St. Bonaventure: only because the Franciscan, sensing danger, made the children leave 15 minutes before the usual time."
There were also explosions in Damascus. "These are bad signs for religious minorities," the Vicar said. However, he added, "I am confident that peace can return: for this we Christians count on constant praying."
Some Jesuits who have decided to stay in the city are giving a "heroic witness," promising to bring comfort and humanitarian aid to people in need, the agency said.