"At this rate, if the targeted violence continues, there will be no Muslims left in much of the Central African Republic," Peter Bouckaert, emergencies director at Human Rights Watch, said in a statement Wednesday.
Seleka, a Sunni rebel coalition, toppled the government in March. Seleka's former President Michel Djotodia, who agreed to resign in January, lost control of the rebel force after the coup. Conflict has approached the brink of civil war since the Christian anti-balaka militia took up arms against their Sunni rivals.
The rights group said the Christian militia has used language suggesting they're trying to eliminate the Muslim population in CAR, one of the poorest nations in the world.
"People whose families have peacefully lived in the country for centuries are being forced to leave, or are fleeing the very real threat of violence against them," Bouckaert said.
The International Criminal Court last week said it opened an investigation into ongoing atrocities in CAR.
France and the European Union have authorized military units for deployment to CAR to help with an African Union peacekeeping operation.