The first group of stranded South Sudanese, who have been living in makeshift shelters in Sudan, are to be repatriated to the southern capital, Juba, today, Agence France Presse reported.
The International Organization for Migration (IOM) in Sudan said there were minor delays to flights, but that the voluntary repatriation would go ahead.
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A group of 400 South Sudanese traveled by bus to Khartoum from the Kosti way-station in White Nile state, where an estimated 15,000 people are camped in crowded conditions.
Local officials had set a deadline for South Sudanese residents to leave Sudan, calling them a security risk.
According to Reuters, tens of thousands of South Sudanese lost their jobs in Sudan after the south broke away and became independent in July 2011.
The news agency estimates that 500,000 are without residency papers in the north, and are technically illegal.
Meanwhile China today sent an envoy to Khartoum for talks, after the country supported a UN resolution aimed at putting an end to border fighting between the two Sudans, AFP reported.
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And the United Nations secretary general Ban Ki Moon called on Sudan to pull its troops from the disputed region of Abyei, after South Sudan withdrew its police from the area.