Wednesday's attack happened at the Church of Fatima in the capital Bangui, following clashes in a nearby neighborhood between Muslim and Christian fighters.
At least 10 people were killed. The bloodshed is largely blamed on Muslim rebels. Assailants sprayed bullets and hurled grenades at those sheltering in the Church, which had become home to thousands of Christians displaced by the country's violence. One of the dead was a 76-year-old priest.
"We were in the church when we heard the shooting outside," the Rev. Freddy Mboula told The Associated Press.
"There were screams and after 30 minutes of gunfire there were bodies everywhere."
Peacekeepers from the African Union arrived in armored vehicles to take control of the area after the attack.
The majority Christian country has been plagued by violence since March last year, when largely Muslim Seleka rebels ousted the president. The violence has killed thousands and displaced nearly a million people.
Fears are growing that this latest attack could spark reprisal attacks on Bangui's few remaining Muslims, most of whom fled the city earlier this year. The group has been targeted by violent Christian militias in the ongoing civil conflict.
It was the worst attack blamed on Muslims in the capital since the Seleka rebels relinquished power in January. A transitional government, led by interim President Catherine Samba-Panza, has been given the task of organizing elections no later than early next year - but there are doubts this can happen, given the ongoing violence.
Out of the 2000 French soldiers deployed to the country, at least 700 have been assigned to patrol Bangui streets in light armored vehicles.
Paris annouced earlier this month that French journalist Camille Lepage was murdered while on assignment in the Central African Republic.
jr/jm (Reuters, AP, AFP)