An airlift of up to 15,000 ethnic South Sudanese began on Monday from Khartoum, an AFP correspondent said.
The first plane chartered by the International Organisation for Migration (IOM) took off at 0615 GMT carrying around 160 South Sudanese, some of whom have spent their entire lives in the north.
They are among a group of 12,000-15,000 South Sudanese who have been waiting for transport South from the Kosti way-station 300 km from Khartoum.
Kosti became home to the biggest single concentration of South Sudanese awaiting transport South, with many living in makeshift shelters or barn-like buildings for up to a year. The Governor of the Kosti area declared the migrants a security threat and initially gave them a May 5 deadline to leave, sparking concern from the United Nations and the IOM which has already helped thousands of South Sudanese to head South. Officials extended the deadline to May 20 but then told the IOM to disregard the time limit after plans for the airlift were devised.
