"The evacuation of our citizens has commenced. Seven buses have left Khartoum and they are heading to Egypt," Manzo Ezekiel, spokesman for Nigeria's National Emergency Management Agency (NEMA) told AFP.
Around 40 buses have been hired to convey stranded Nigerians from the war-torn nation.
Ezekiel said 3,500 Nigerians, including students, were to be transported firstly to Aswan in neighboring Egypt.
Officials said there are more than 5,000 Nigerians in Sudan.
Onimode Bandele, NEMA special duties director, told AFP on Tuesday officials including embassy staff were at the collection center to assist in the process.
"We are looking at over 5,000 Nigerians, but right now we are talking of 3,500, including students, that will be transported in buses to Aswan in Egypt," he said.
He said the journey "will take some time because Khartoum to Aswan is about 1,200 kilometers.
After arriving in Aswan evacuated Nigerians would be airlifted to the capital Abuja.
Local Nigerian carrier Air Peace had volunteered to transport the Nigerians free of charge, he added.
Bandele said the government had taken all necessary measures to ensure the safety of the Nigerians.
Since fighting erupted, at least 427 people have been killed and more than 3,700 wounded, according to UN agencies, which also reported Sudanese civilians fleeing to Chad, Egypt and South Sudan.
Nigeria Evacuates Citizens From Sudan
FILE: In an earlier evacuation from the Sudan capital, people gather as they flee clashes between the paramilitary Rapid Support Forces and the army in Khartoum, Sudan April 24, 2023.
LAGOS - Nigeria on Wednesday started evacuating the first of around 3,500 of its nationals, mostly students, from Sudan to neighboring Egypt Wednesday as a fragile ceasefire allowed foreigners to flee, emergency services said.