The violence was triggered by the killing of 17 Muslims at a camp in the central Bambari region on Monday, by gunmen claiming to be from a mostly Christian militia called the anti-balaka.
"Nearly 50 people have been killed since Monday during violence in the Bambari region and nearby villages," the officer from the African Union force MISCA told AFP. "Most of the victims were shot or stabbed to death."
Peacekeepers say there have been a series of tit-for-tat attacks in the region following the massacre.
"Apart from attacks aimed at civilians and the burning down of houses, there are also clashes that appear to be coordinated attacks by armed groups," both from Christian and Muslim militias, said the officer, who spoke on condition of anonymity.
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The Central African Republic has seen more than a year of unrest since the mainly Muslim Seleka rebel group seized power in a coup, unfurling a vicious cycle of violence with largely Christian militias.
Bambari, where the ex-Seleka rebels have established their new headquarters, is being closely watched by French soldiers from the Sangaris mission and African peacekeepers from the MISCA force, although they have not been able to contain the violence.
Fighting in a village outside Bambari in early June left at least 22 people dead, both Muslim and Christian, according to security officials and last week 10 bodies showing signs of torture were found in a river in the region.
In a report released yesterday, advocacy group the International Federation for Human Rights (FIDH) said that "war crimes and crimes against humanity" continue to be carried out as the "conflict of impunity" rages in the former French colony.