For his part, the ousted Bozize has denied having any connection with or control over the anti-balaka forces.
And the man who toppled him, Djotodia, in a televised speech on New Year's Eve, condemned "all forms of xenophobia and at the same time the large-scale returns of long-term-resident foreigners to their respective countries. Because our country is and will remain a place of refuge and hospitality for all peace-loving people."
The exodus will have major ramifications for both CAR and Chad. People of Chadian origin - together with those from Cameroon and Nigeria - form the backbone of the trading and livestock sectors in CAR.
Major economic problems lie down the road, according to Richard Pouambi, chief of staff in CAR's Ministry of Communications.
"Those who are leaving are traders, they are the tax payers, and without them the state will have trouble filling its coffers. Billions of francs [hundreds of thousands of dollars] are spent every day in KM5," he said, referring to Bangui's largest market.
Already, some foodstuffs are running short and speculators are buying up staples. Prices are generally rising. Civil servants have not been paid for three months.
Meanwhile, the numbers of people entering Chad "are moving upward very, very fast; the latest number is 19,000 as of 8 January", Qasim Sufi, the head of operations in Chad for the International Organization for Migration (IOM), told IRIN. Sufi added that the total caseload might end up being five times that number.
The current figures include 200 unaccompanied children, he said.
After registration by the government, new arrivals are taken to transit centres in the capital and near the CAR border, where they are provided with medical care, food, and, for those who are traumatized, psycho-social support.
After a few days, the migrants are transported to their places of origin. As it with 150,000 Chadian migrants who returned from Libya between 2011 and 2013, IOM plans to help with economic reintegration and projects to ease tensions with host communities.
"However, for those who left the country long ago or were even born in the CAR, a different approach has to be found to address their needs, and IOM... is currently coordinating with the government of Chad to come up with a clear strategy for this latter group," said Sufi, in an email.
He added that because the new caseload remitted large sums of money to relatives in Chad while living in CAR, "this migration crisis will have a bigger impact on the economical aspect of the country compared to the Libya crisis, where most of the migrants were predominantly in very low-income-generation sectors, such as drivers, farmers, guards, etc."
He added: "Considering the estimated number of Chadian migrants in the CAR (more than 100,000), it is [a] huge challenge to both the government and the humanitarian community that is trying to meet their needs.
"For this reason, IOM, as the migration and the frontline agency, has just launched an appeal for funding (US$17.4 million) to try to meet their immediate needs, including the live-saving component of their evacuation from the CAR, and bring to them back to the safe havens in their places of origin."
[ This report does not necessarily reflect the views of the United Nations. ]