Sudan has accused a senior UN official of fabricating allegations of human rights abuses in the troubled western province of Darfur.
Thousands have been driven from their homes in Darfur by fighting
The Humanitarian Affairs Ministry said claims by Mukesh Kapila were "a heap of lies", Sudanese radio reported.
On Friday, Mr Kapila described the situation in Darfur as the worst humanitarian crisis in the world today.
He accused government-backed Arab militias of systematically burning villages and raping women in the area.
More than 100 women were raped in a single attack carried out by Arab militias in the region, he said.
Speaking to the BBC, Mr Kapila, the UN co-ordinator for Sudan, had said the conflict had created the worst humanitarian situation in the world, with more than one million people affected by "ethnic cleansing".
He said the fighting was characterised by a scorched-earth policy and was comparable in character, if not in scale, to the 1994 Rwandan genocide.
"It is more than just a conflict. It is an organised attempt to do away with a group of people," he said.
Mr Kapila also called for more aid and for urgent international intervention to bring about a ceasefire in the war.
However the Sudanese government said that, in his comments, Mr Kapila had "deviated from the virtues which a resident representative should have, that is neutrality, and transcended to open political work".
It said it had carried out humanitarian work which had been commended by UN
officials in Sudan and visiting Western delegations and which had led to "noticeable stability and the return of tens of thousands of displaced persons and refugees", the Associated Press news agency reported.
Sudanese radio said the government and the UN had agreed to end Mr Kapila's mission in Sudan.
Arab militias, backed by the government, have driven hundreds of thousands from their homes in Darfur, in retaliation for a rebellion launched a year ago by two armed groups.
They had accused the Arab-dominated government of ignoring the black African inhabitants of Darfur.
More than 100,000 people have fled across the border into Chad, but have continued to face cross-border raids.
To compound the humanitarian problem, aid agencies can only reach small parts of Darfur and are subject to attacks.
The fighting in the west of Sudan has intensified as government peace talks to resolve the 20-year war with southern rebels are nearing an end.
But the UN is concerned that this conflict could undermine the peace talks in Kenya.