A first convoy of 13 buses left Sudan's capital Khartoum on Thursday for the Egyptian border with a plan to fly on Friday to Nigeria, but the group was refused permission to cross the frontier.
Egyptian authorities on Monday agreed to let the evacuees cross after Nigerian President Muhammadu Buhari intervened, the Nigerians in Diaspora Commission said in a statement on Twitter.
Nigeria's National Emergency Management Agency (NEMA) confirmed the group were already in Egypt, but could not give details on when they would be flown home.
That convoy would no longer travel to Egypt, but to Port Sudan, a city located on the Red Sea, 675 kilometers (420 miles) from Khartoum, from where they should then be flown back to Nigeria, NEMA spokesman Manzo Ezekiel told AFP on Tuesday.
According to Nigerian authorities, the evacuation plan is for more than 3,500 nationals, but their total number could be greater. Many of the Nigerians in Sudan are students.
Sudan was plunged into fighting on April 15 between two generals who have been in charge of the country since a military coup in 2021.
Army chief Abdel Fattah al-Burhan and Rapid Support Forces (RSF) paramilitary commander Mohamed Hamdan Dagalo had agreed to extend a three-day ceasefire. However, air raids, shooting and explosions shook Khartoum, the capital, again on Monday.