UN resident coordinator and humanitarian coordinator Ali Zaatari and the UN Development Programme country director Yvonne Helle have been asked to leave, said a UN staffer who spoke on condition of anonymity, yesterday.
United Nations spokesman Stephane Dujarric said the body has protested the expulsions.
"The UN has filed a protest with the government of Sudan following their decision to request the departure of two senior UN officials from the country," Dujarric told AFP.
"The sanctioning of United Nations personnel sent to Sudan to carry out their duties in accordance with the United Nations Charter is unacceptable," Dujarric added.
It was unclear clear why the UN officials were asked to leave, or when they would have to exit the country. The UN staffer declined to provide further details.
The UNDP and Sudanese foreign ministry did not respond to requests for comment.
Zaatari, a Jordanian national, had been in Sudan for nearly two years, and Helle, who is from the Netherlands, had spent about a year heading the UNDP's office in the country.
Ties between the two have frayed over Khartoum's anger at UNAMID's attempts to investigate a report that government troops raped 200 women and girls in a village in the war-torn western region on October 31.
Sudan demanded UNAMID form an "exit strategy" from Darfur, where they have been deployed since 2007, and ordered it to shut a human rights office in Khartoum last month.
Zaatari and Helle's expulsion are the latest in a string of incidents with foreign aid and humanitarian workers in Sudan.
The UN and international NGOs provide aid to some of the areas of Sudan worst affected by the conflicts wracking its peripheries.
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