Michel Djotodia, former Seleka rebel leader who seized power in a March coup, called for an end to the "massacres" as violence has swelled between Muslims and Christians.
"Love one another! We find that in the Bible and the Koran," said the interim president, flanked by local religious leaders from the Christian and Islamic faiths.
He also banned all illegal demonstrations in Bangui and accused ousted president Francois Bozize and his supporters of being behind the violence which "massacres innocent Central Africans."
The exchange occurred as the Chadians, mainly because they are Muslim, face accusations of complicity with the Seleka rebels who overthrew Bozize in the predominantly Christian country now gearing up for Christmas.
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Lieutenant-Colonel Pontien Hakizimana, head of the Burundian contingent in the African force MISCA, told AFP in Bujumbura that his men were disarming former rebels when Chad's MISCA troops threw a grenade and opened fire on them, prompting some Burundian elements to return fire, wounding three Chadians.
"On Monday morning we intercepted six armed ex-Seleka and we disarmed them," Hakizimana told AFP from Bangui.
"Then the Chadians left with the ex-Seleka, firing in all directions," he said, adding some of his men came under fire and retaliated, wounding three Chadians.
"The Chadians soldiers came back in greater numbers in the afternoon and attacked our positions," Hakizimana said, adding that Burundian troops had repelled them.
There was no immediate comment from the Chadian contingent.
A military source in Bujumbura said relations between the Burundians and the Chadians had been strained ever since the Chadians in the MISCA had been re-deployed outside the capital and the Burundians tasked with securing Bangui.