He confirmed to Daily Trust that there are about 2000 Nigerians at the embassy in Bangui but that officials were working to ensure their return.
"The government is working seriously to evacuate them and we are aware that there are 2000 Nigerians presently in our embassy in Bangui," the permanent secretary said.
When asked when the process will begin, he said, "By the Grace of God before the end of this week, the process will start."
The CAR violence broke out in March following the toppling of President Francois Bozize by then-rebel leader Michael Djotodia who is now the country's leader.
About 1,000 people have been killed in tit-for-tat clashes in Bangui in December and about 370,000 people, nearly half the city's population, have been displaced, aid agencies say.
Although community leaders said many Nigerians were among the dead, the Federal Government said those killed were descendants of Nigerians.
The African Union has sent nearly 4,000 troops to CAR while France, the former colonial power, has also deployed 1,600 soldiers there in an attempt to quell violence.