The vigilantes "surrounded the town early this morning and shots from light and heavy firearms could be heard in several areas of Bouar", an officer said on condition of anonymity. (Agencies)
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.
The clashes between the vigilantes and the former Seleka rebels which are now part of the Central African armed forces "killed four among the self-defence groups and left several people wounded in both camps", said the military official.
Fighting was heard in several areas of the largely deserted town throughout the morning, said the officer, who was unable to say whether it had caused any casualties.
By mid-afternoon, "the army had taken control of the city", Bouar's mayor Ali Aoudou Moumini said.
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.
Awalou Mamadou, a local shopkeeper in Bouar, which is located some 400 km northwest of the capital Bangui, estimated the number of attackers at between 300 and 500 men.
Maxime Lalai, a local civilian, said "the attackers have surrounded the town, we are trapped, we don't know which direction to flee to".
On October 21, the Central African Republic's neighbours pleaded for more robust action from a regional peacekeeping force, which is ill-funded and has so far failed to make an impact.
The vigilantes "surrounded the town early this morning and shots from light and heavy firearms could be heard in several areas of Bouar", an officer said on condition of anonymity.