"Clashes broke out Friday between security forces sent from Bangui to Bomboro (south of the capital), and the 'anti-balaka' self-defence group," an army official said on condition of anonymity.
The official said the fighting left six dead among the ranks of the vigilante.
The anti-balaka ("anti-machete" in the local Sango language) was formed by local residents exasperated by the abuses committed by members of the ex-rebel Seleka group.
The now disbanded Seleka toppled Francois Bozize in March and its leader Michel Djotodia subsequently became the country's first Muslim president.
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Cases of executions, rape and looting by ex-Seleka fighters in the aftermath of the coup have stoked sectarian tension in the former French colony, where the population is 80 percent Christian.
The army official said the embattled central government responded to growing concern by Bomboro residents over the vigilante's activities by dispatching troops.
Clashes between rogue former rebels and vigilantes in the northwest of the country earlier this week killed nearly 50, according to a security official.