An "exceptional" airlift of almost 12,000 South Sudanese ended with a final flight from Khartoum on Wednesday but thousands more continue to live in makeshift conditions while they, too, await transport South, officials said.

One hundred Southerners took the last chartered plane from Khartoum to South Sudan's capital Juba at 1000 GMT, said Jill Helke, chief of the International Organisation for Migration (IOM) in Sudan.

"With the 100 people who fly today, we will have moved 11,840 people in 24 days on 79 flights," she told a ceremony at the airport before the departure.

"It is a remarkable feat."

IOM began more than three weeks ago flying out Southerners, whom local authorities ordered to leave, from the Kosti way-station 300 kilometres (190 miles) from Khartoum.

Kosti became home to the biggest single concentration of South Sudanese needing transport, 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 5 May. That sparked concern from the United Nations and the IOM, which has already helped thousands of South Sudanese head to South Sudan, which became independent last July.

Officials extended the deadline to 20 May but then told the IOM to disregard the time-limit after plans for the airlift were devised.

Helke said the flights—up to four a day—were "an exceptional operation to respond to an exceptional set of circumstances".

The UN refugee agency said on Tuesday that an increasing number of South Sudanese—some hoping for an operation similar to the Kosti airlift—are living in crude shelters in the Sudanese capital.

Estimates from community leaders say that up to 38,000 South Sudanese are now staying in so-called "departure points" around Khartoum, said Philippa Candler, assistant representative for protection with the UN High Commissioner for Refugees (UNHCR) office in Sudan.