The head of the United Nations mission in Sudan, Jan Pronk, is expected to leave the country after being ordered out by the government.
The expulsion was ordered after Mr Pronk wrote in his blog that Sudan's army had suffered defeats in the Darfur region and its morale was low.
Mr Pronk's relations with the Sudanese government were shaky before this row.
Sudan's government had given Mr Pronk until midday Wednesday to leave, but UN Secretary General Kofi Annan has recalled him to New York for consultations.
It was Mr Pronk's comments on his personal website that angered the Sudanese government.
"Morale in the government army in north Darfur has gone down," he wrote. "Some generals have been sacked; soldiers have refused to fight."
He said the Sudanese army had lost two major battles recently to rebel groups in the western region and that Arab militias - who have been accused of atrocities - were being mobilised in violation of UN resolutions.
The army led calls for Mr Pronk's expulsion, calling his remarks psychological warfare.
Junior Foreign Minister Sammani al-Wasila told the BBC that Mr Pronk had strayed beyond his mandate and lost his neutrality.
"It is not his right to comment," he said. "His role as personal envoy to the secretary general means he should be neutral to help solving problems, rather than creating problems."
Britain has condemned Mr Pronk's expulsion and urged Sudan to reconsider.
"This step is counter-productive and will contribute nothing to solving the problems of Sudan," said Foreign Office Minister Lord Triesman.
In Brussels, European Union spokesman Amadeu Altafaj Tardio said: "The presence of the United Nations is vital to hundreds of thousands of citizens of the Darfur region."
Sudan's Minister of State for Foreign Affairs, Ali Karti, told the BBC that it was Mr Pronk, not the UN, that was the problem.
"It is not the United Nation's activities in Sudan," he said. "They are welcome."
'No free voices'
There was also opposition to the move within Sudan.
"It is a wrong decision which is going to worsen the situation of Darfur instead of solving it," said Yasser Arman, the spokesman for the southern Sudanese government.
And Khalil Ibrahim, a senior member of the rebel National Redemption Front, told Reuters news agency the decision came from the army.
"They don't want to leave any free voices in Sudan," he said.
The BBC's Jonah Fisher says that although in theory there is a coalition government in Khartoum, this episode has illustrated just how strong the military remains.
Their pride hurt by Mr Pronk's comments, the Sudanese army has succeeded in removing a man who spoke openly about the government's continuing role in atrocities, our correspondent says.
BBC World Service broadcasts to Juba in Southern Sudan and surrounding areas in Arabic on 90.0 FM and in English on 88.2 FM. In Northern Sudan: Khartoum 91.0 FM, Al Ubayyid 91.0 FM, Port Sudan 91.0 FM and Wad Madani 91.5 FM.
“Violence will bring no victory. For the sake of the Darfur civilians, all parties to the conflict have to stop resorting to violence. This is the absolute priority.” - Luis Moreno-Ocampo, Prosecutor of the International Criminal Court, 05 June 2009
"APPREHENSION" by Rob Rooker. Painted on a wall in Maridi, Sudan. The image is of a young Nuer boy looking up among a crowd of people. Click on image for more details. Cards & prints of Rob's paintings can be purchased online at Imagekind.com