The victims were among hundreds who sought refuge from fighting in the capital city at the Church of Fatima. Members of the Seleka coalition, who were removed from control of the nation's government five months ago, were blamed for the attack.
Witnesses said rebels approached the church Wednesday and began throwing grenades and indiscriminately shooting.
The city is largely Christian, since most Muslims have left in what the United Nations called a campaign of ethnic cleansing, and are among the nearly one million people in the country who are refugees. It is feared the incident may spark reprisals against the remaining Muslim population.
The crisis in the Central African Republic, since January when the primarily Muslim government was forced from power, has typically involved armed Christian groups targeting Muslims. After the Islamist regime seized power in March 2013 and kept it for 10 months, rebels looted and killed the Christian population of the city.