Gunmen armed with grenades targeted Notre-Dame de Fatima Church on the border of the predominantly Muslim PK 5 area where 21 people were killed during clashes last month.
Witnesses said churchgoers were forced to escape through a hole made in the church wall by police.
"Filled with panic, some Christians began to flee until bullets and grenades began to fall in the parish grounds, trapping those who remained in the compound," Moses Aliou, a priest at the church, told Reuters.
CAR has faced several years of both ethnic and religious conflict since 2013 when mainly Muslim Seleka rebels ousted President Francois Bozize.
Retaliation killings are common occurrences, spear-headed largely from Christian communities, and Muslim "self-defence" groups.
This isn't the first time the church has been attacked.
In 2014 gunmen with grenades killed a priest and some worshippers.
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