The International Organization for Migration (IOM) said it would begin to airlift some of the 33,000 people from other African nations who need "urgent" help in the Central African Republic.
Some 2,500 Chadians are sheltering in a transit camp adjacent to Bangui airport, living in overcrowded and unsanitary conditions, the organisation said.
The group said it was reponding to appeals from neighbouring African countries.
Search underway for new Central African Republic president
Meanwhile, the search is on for a candidate to replace Michel Djotodia, who resigned as president of the Central African Republic after failing to pull the country out of anarchy.
Under intense diplomatic pressure, Michel Djotodia stepped down yesterday during a special regional summit in Chad.
Djotodia had come under fire for failing to rein in the mainly Muslim rebels who brought him to power last year and whose abuses triggered retaliatory violence by Christian militias.
Prime Minister Nicolas Tiangaye, whose bad relations with Djotodia had crippled the state's ability to take any decisive action against armed gangs, also quit.
UN urges more troops be sent to Central Africa
UN Secretary General Ban Ki-moon has called on the African Union to speedily provide promised troops to help curb the "terrible crisis" in the country.
France has deployed 1600 troops in the country to support the African Union MISCA force, which is meant to have up to 6000 troops but has not yet reached 3500.
European nations on Friday agreed in principle on a plan to launch a joint military operation in the country, with a final decision expected on January 20, an EU source said.
Candidates to replace Djotodia have yet to emerge, but the interim parliament is due to hold a special session Monday.
French Defence Minister Jean-Yves Le Drian urged lawmakers to decide "as soon as possible".
Chad is seen as having more than tacitly backed Djotodia's coup but, true to its reputation as the kingmaker of Bangui politics, it moved to sideline him when he failed to deliver.
All 135 Central African lawmakers were flown to the summit of the regional ECCAS grouping on Thursday at the behest of Chadian President Idriss Deby Itno.