The UN's envoy to Sudan, Jan Pronk, has been recalled to New York for consultations following Khartoum's demand that he leave within three days.
Mr Pronk has been criticised by Sudan's army
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.
A UN spokesman said Mr Pronk was expressing his personal views.
Sudan is resisting strong international pressure to allow UN peacekeepers in to try to end the conflict in Darfur.
Sudan's government had given Mr Pronk until midday Wednesday to leave, but with UN Secretary General Kofi Annan recalling him for consultations, he will now leave late on Monday.
Sudan's Minister of State for Foreign Affairs, 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. "The second thing, the false information he is giving and the interference in matters - he has got nothing to do with it. Enough is enough.
"His role as personal envoy to the secretary general means he should be neutral to help solving problems, rather than creating problems."
Mr Pronk is not guaranteed an entirely sympathetic hearing from his boss in New York, says the BBC's Jonah Fisher in Khartoum.
Mr Pronk's website has got him into trouble before, our correspondent says, and he has ignored requests from within the UN to stop writing on it.
He was already at loggerheads with Khartoum over attempts to get UN peacekeepers into Darfur.
This time he angered the Sudanese by writing on his personal website a week ago that "morale in the government army in north Darfur has gone down. 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 were being mobilised in violation of UN resolutions.
The Janjaweed militias are accused of widespread atrocities, even genocide.
The army said Mr Pronk's remarks amounted to psychological warfare and demanded an apology.
More than 200,000 people are thought to have died and two million have been displaced as a result of the three-year conflict in Darfur.
The UN Security Council has passed a resolution calling for 20,000 troops to be sent to Darfur to replace the 7,000 poorly equipped African Union troops who have failed to end the conflict.
But the BBC's Laura Trevelyan says that UN officials privately acknowledge that all they may be able to do is provide back-up to the AU force.
The Janjaweed are accused of ethnic cleansing in Darfur
Sudan has said it will not allow UN peacekeepers on its territory, calling it a bid to restore colonial rule.
Britain 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 official news agency, Suna, said Khartoum remained "committed to co-operate" with the UN, and would work with Mr Pronk's successor.