“As of the end of yesterday we have airlifted about 3,600,” an IOM officer told AFP.
She said the number of daily charter flights between Khartoum and the South Sudanese capital Juba has doubled to four since the operation began on May 14, and could peak at six in coming days.
The agency is planning to fly a total of 12,000 Southerners who have been staying at the Kosti way-station 300 kilometres (190 miles) from Khartoum.
Kosti became home to the biggest single concentration of South Sudanese needing transport South, with many living in makeshift shelters or barn-like buildings for up to a year, and dependent on foreign aid.
The governor of the Kosti area declared the migrants a threat to security and the environment and ordered them out by May 5, sparking concern from the United Nations and the IOM which has already helped thousands of South Sudanese head South.
Officials extended the deadline to May 20 but then told IOM to disregard the time limit after plans for the airlift were devised.
“We should be able to finish up by the end of the month,” said the IOM officer, declining to be named. “It’s going pretty well”.
She said the agency, which depends on donor funding, has now received commitments for all of the roughly $5.5 million cost of the airlift.
The South Sudanese in Kosti are among about 350,000 ethnic Southerners who the South Sudanese embassy estimates remain in the north after an April 8 deadline to either formalise their status in the north or leave the country.
Many have spent their entire lives in the north or came to Sudan when they were children, as millions fled a 22-year civil war. The war ended in a 2005 peace deal which led to South Sudan’s independence last July.
Hundreds of thousands made their way from Sudan to South Sudan ahead of the separation or in subsequent months.
Most of the Southerners in Kosti did not have their own means to arrange transportation, said IOM, which planned to move thousands of them by barge until Sudan’s military expressed security concerns.
In March and April Sudan and South Sudan fought a border war, raising fears of wider conflict amid a climate of heightened nationalism in the north.
A UN Security Council resolution on May 2 ordered both sides to cease hostilities and to resume negotiations on unresolved issues including the status of each country’s nationals in the other country.