Sudan's government has asked the UN-African Union force in Darfur (Unamid) to shut its human rights office, the joint peacekeeping mission says.
The move comes amid tensions over the mission's attempt to investigate allegations of mass rape by Sudanese troops in the Darfuri village of Tabit.
The authorities initially refused access to the village; when Unamid did get there it found no evidence.
Darfur has been in conflict since 2003, when rebels took up arms.
Unamid has a mandate to stem violence against civilians and currently has nearly 16,000 personnel deployed in the troubled western region.
The conflict in Darfur is now being waged on many fronts and by different groups involving pro-government forces, rebels, militias and involving inter-ethnic violence.
Unamid said it was working with the authorities to "clarify the role" of its human rights office, based in the capital, Khartoum.
On Tuesday, the Sudanese foreign ministry confirmed that it had also asked the UN to prepare an exit plan for Unamid from Darfur.
This was not in response to the allegations of mass rape but part of a long-term strategy following an improvement of the security situation in Darfur and concerns at the "serious violations that were perpetuated by Unamid" over the years, the state-run Suna news agency reports.
But it came days after Unamid was denied permission to make a second visit to Tabit, about 45km (28 miles) south-west of Fasher city, to further investigate local reports that soldiers had raped 200 women and girls last month.
According to the AFP news agency, an internal Unamid report said Sudanese soldiers had intimidated villagers during their visit on 9 November.
Government restrictions make it difficult for foreign aid agencies and journalists to work in Darfur.
The UN estimates that about 300,000 people have died because of the conflict, mainly of disease, and more than two million have fled their homes.
The International Criminal Court (ICC) has issued an arrest warrant for President Omar al-Bashir for suspected genocide and war crimes in Darfur.
Khartoum has dismissed the charges and refused to recognise the ICC.
It says the conflict has killed about 12,000 people and the number of dead has been exaggerated for political reasons.
Talks between the government and some Darfuri groups began in Ethiopia over the weekend.