A Christian cathedral in Bambari was attacked on Monday, leaving at least 20 dead and 25 injured.
Survivors say members of the Seleka rebel group and Muslim civilians attacked St. Joseph's Cathedral around 1400 GMT. Between four and six thousand Christians had been living in the church.
A nun was able to call a reporter during the grisly attack.
"They came in. They are killing people," she told Reuters before the phone disconnected. The news agency reported that attempts to reach the nun were unsuccessful.
A French military spokesman Gilles Jaron said that their soldiers intervened on behalf of the Christians at around 1500 GMT.
"We immediately returned fire and in all likelihood inflicted losses on [the Seleka fighters]," Jaron told Reuters.
"Currently we are present around the bishopric to protect that population [of Christians]."
A Cathedral priest, Rev. Firmin Gbagoua, said that the Seleka believed that Christian militia members known as anti-balaka or anti-machete, were inside the church.
Seleka spokesman Ahmat Negad said that a Muslim community was recently attacked by anti-balaka, and one Muslim civilian was killed. Negad said the assault at St. Joseph's Cathedral was in reprisal.
"All we did was retaliate," he said, according to Reuters.
Archdiocese of Bangui vicar general Rev. Jesus Martial Dembele said the onslaught was devastating.
"We don't have the exact death toll yet, but many people have been killed. As I'm speaking to you, they are still there," he reported Tuesday.
Seleka's military headquarters is based in Bambari. Frequent conflicts have resulted in thousands of deaths and displacements in the landlocked country.
French foreign minister Le Drain called for peace between the Seleka and anti-balaka.
"To avoid clashes between groups that seek only hatred and vengeance, these groups must accept a peace process, accept a ceasefire," he said.
The Seleka overthrew the government in March 2013, but relinquished power in January. Violence continues despite 6,000 African Union peacekeepers and 2,000 French soldiers, according to Reuters.