About 400 people will be brought to Khartoum by bus from the way-station of Kosti, about 300 kilometres (190 miles) south of the capital, ahead of a major airlift early on Sunday, the International Organisation for Migration (IOM) Sudan chief Jill Helk said. "They're moving in a convoy," escorted by local government agencies, Helke told AFP.
After staying overnight in a Khartoum-area government-run transit centre, they are to board three aircraft shortly before sunrise on Sunday, at 0300 GMT, for the South Sudanese capital Juba.
The IOM estimates that 12,000-15,000 South Sudanese are in the Kosti way-station. Many have been living in makeshift shelters or barn-like buildings, waiting months for their transport home.
The governor of the area declared the migrants a security threat and initially gave them a May 5 deadline to leave, a decision that sparked concern from the United Nations and the IOM, which has already helped thousands of South Sudanese to head home.
Sudanese officials extended the deadline to May 20 but then told the IOM to disregard the time limit after plans for the airlift were devised. If the deadline is enforced, "this becomes a deportation and we will not have any part in it," Helke said.
The South Sudanese in Kosti are among about 350,000 ethnic Southerners whom the South Sudanese embassy estimates remain in the north after an April 8 deadline for them to either formalise their status or leave Sudan.
Hundreds of thousands of others have already gone to the South, which separated last July.
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