The vigilantes "surrounded the town early this morning and shots from light and heavy firearms could be heard in several areas of Bouar," the officer told AFP on condition of anonymity.
The self-defence groups, who call themselves "anti-balaka" (anti-machete, in the local Sango language), were carrying machetes of their own as well as various other weapons, he said.
These groups were formed in response to killings, looting and abuse committed by those ex-rebels who did not integrate the army after a coup in March but went rogue, sowing terror across the country.
By mid-afternoon, "the army had taken control of the city", Bouar's mayor Ali Aoudou Moumini, told AFP by telephone.
Moumini said the few people who had not fled before the attack remained holed up at home.
The head of the now disbanded rebel Seleka group, Michel Djotodia, was installed as the impoverished country's first president to hail from the Muslim minority in August.
Many ex-Seleka commanders wreaking havoc in the Central African Republic are Muslims and the creation of vigilantes to combat them has sparked fears of growing sectarian strife.
Maxime Lalai, a local civilian who spoke to AFP by telephone, said "the attackers have surrounded the town, we are trapped, we don't know which direction to flee to".
Ali Camara, who works for the international non-governmental organisation Cordaid, said he went to take refuge in a church, "but it is full there... I went back to my home where I stayed on the floor with my family.
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