"More than a dozen people" were killed in an assault in the southeastern town of Zemio, Jean-Alain Zembi, a priest, told AFP.
Janjaweed militia and armed Fulani tribesmen attacked police and a hospital and set fire to houses, also stealing people's possessions, he said.
"The Moroccan contingent of the MINUSCA force (UN mission) is trying to protect civilians," said Zembi, who wrote on his Facebook page that the attacks constituted crimes against humanity.
There were also clashes on Tuesday and Wednesday in Bria, a central town, a hospital official told AFP, referring to "dead and wounded among civilians".
A MINUSCA spokesman confirmed there had been clashes and that the force had intervened in what remains a tense situation.
Aid groups on Tuesday urged the United Nations to take "immediate action" in the Central African Republic, saying the conflict-wracked nation is "teetering on the brink of catastrophe".
In a letter addressed to UN Secretary-General Antonio Guterres, six humanitarian organisations expressed their "grave concern about the rapid deterioration of the security situation" in the country.
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