One predominantly Peul faction of the mostly Muslim Seleka group has been fighting since late 2016 with another faction that has aligned itself with the Christian anti-Balaka group as they are vying for control of the central part of the country, the rights group said.
"Civilians on all sides are exposed," said Lewis Mudge, Africa researcher at Human Rights Watch.
The death toll is likely higher because many people remain missing, the rights group said after a visit to Ouaka province in April.
Central African Republic descended into sectarian conflict in 2013.
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The latest fighting began in February, when anti-Balaka fighters killed at least 16 Peul civilians in the village of Ndoussoumba, and in March attacked three Peul men in Yassine, a town northeast of Bambari and under control of the Peul Union for Peace in the Central African Republic, Human Rights Watch said.
Fighters with the UPC then attacked residents who moved to Yassine for safety, killing some 18 people. The group killed civilians in other villages around that time, Human Rights Watch said.
The United Nations mission has asked the UPC, which has controlled most of Ouaka province since 2013, to relocate. It is now based about 50 kilometers (31 miles) from Bambari.