The directive was announced Monday after a meeting of the National Security Committee Council (NSCC) chaired by President Kiir held at the presidency in Juba on Monday.
The Minister of Interior and NSCC Spokesperson Michael Chienjiek said the Council listened to the security reports from the chief of defence forces, and other security organs.
"President Kiir ordered those still occupying residential houses of those who are in the UN Protection of Civilians sites to be evacuated immediately to allow the rightful owners to return home," Chienjick further said.
Last November, David Shearer, the Head of the United Nations Mission in South Sudan (UNMISS) said many people living in the UN protection sites have returned to their home areas.
However, he pointed out that many others are still in the PoC sites because they have no land while the land of some IDPs is now taken by others and have nowhere to go to.
"This is the responsibility of the government – both national and local," said Shearer.
"The homes of some people living in PoC sites have also been illegally occupied by others. That is also the responsibility of the government, to ensure these are vacated for families to move back to," he further stressed.
The Interior Minister did not speak about the sexual violence that took place last November.