"All non-governmental organisations, private companies, banks, insurance companies, telecommunication companies, petroleum companies, hotels and lodges working in South Sudan are directed to notify all the aliens working with them in all the positions to cease working as from 15th October," said a government statement, published in several newspapers.
The order said the organisations and companies should advertise the positions -- ranging from receptionists to executive directors -- so that they can be filled by "competent South Sudanese nationals".
South Sudan is also heavily dependent on a network of international aid groups for humanitarian assistance for 1.3 million people who have been internally displaced by the conflict.
The international NGO Global Witness, which campaigns to prevent natural resource-related conflict and corruption, said the order was "disturbing".
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"It is disturbing that the South Sudanese government is attempting to expel trained aid workers at a time of a grave humanitarian crisis," the group said.
South Sudan suffers from a major shortage of skilled workers, with only around a quarter of the population being able to read and write.
Fighting broke out in oil-rich country, the world's youngest nation, in December 2013 following a clash between troops loyal to President Salva Kiir and his former deputy Riek Machar.
The war spread rapidly across the country and has been marked by widespread human rights abuses and atrocities by both sides.