Reports from Bangui say about 30 Chadian residents have been killed, though the Chadian Government issued a statement saying that between 80 and 120 Chadians were "massacred" on Thursday evening.
Government forces ousted rebels from northern Bangui after a week of fighting, but there have been reports of serious violence and looting since then.
The CAR Government accuses neighbouring Chad of being involved in the rebellion launched by supporters of the former army chief, Francois Bozize, who fled to Chad last year after he was dismissed from his post.
The BBC's reporter in Bangui, Joseph Benamse said that Chadians running from the north to the south told him that presidential security forces were targeting them.
There are more than 400,000 Chadians living in CAR, with about 50,000 residing in Bangui, our reporter says.
Looting denied
Meanwhile, the United States has closed its CAR embassy and is withdrawing its diplomats.
The pull-out was ordered despite reports that the rebels were retreating northwards from the capital, Bangui, with the army in pursuit.
US nationals have been told not to travel to the country.
There have been reports of serious violence and looting in the northern suburbs by Congolese fighters supporting President Ange-Felix Patasse.
But the leader of the Congolese rebel group, the Movement for the Liberation of Congo's (MLC) Jean-Pierre Bemba, denied the allegations in an interview with the BBC's Network Africa programme, saying his troops were more than 20 kilometres outside Bangui.
The army, backed by the MLC and Libyan troops, launched its offensive on Wednesday - six days after fighting began between the insurgents supporting General Bozize and troops loyal to President Patasse.
Our correspondent says that many people have been killed in the fighting in Bangui including civilians, rebels and Chadian soldiers fighting alongside them, as well as loyalist troops and Libyan and Congolese fighters who are giving them support.
France has confirmed that General Bozize, who has been in exile there, was back in Paris after a brief visit to Chad.
Government forces have been supported by Libyan troops since a coup attempt against President Patasse in May 2001.