"The government... considers Jan Pronk's mission... in Sudan over and Mr Pronk has to leave Sudanese soil within 72 hours from midday on Sunday," a Foreign Ministry statement said.
"The reason is the latest statements issued by Mr Pronk on his website regarding severe criticism of the Sudanese Armed Forces and the fact that he said the government of Sudan is not implementing the Darfur peace agreement," Foreign Ministry spokesman Ali al-Sadig said.
He said the Foreign Ministry met with Mr Pronk on Sunday and informed him of its decision. The ministry statement said the government will continue to cooperate with the United Nations.
Mr Pronk has had previous problems with the government because of comments he published in a web log diary carried by his website www.janpronk.nl. The latest entry said Darfur rebels had beaten the army in two major battles in the last two months.
He said generals had been sacked, morale was low and soldiers were refusing to fight in North Darfur. The army was furious and issued a statement on Friday calling Mr Pronk a danger to the nation's security.
One army source said they were asking President Omar Hassan al-Bashir, the commander-in-chief of the army, to expel Mr Pronk.
Mr Al-Sadig said rebels would consider Mr Pronk's comments as encouragement to continue their military campaign.
Mr Pronk has been summoned to New York for consultations with UN Secretary-General Kofi Annan.
But Khalil Ibrahim, a senior member of the rebel National Redemption Front (NRF), told Reuters the decision to expel Mr Pronk did not come from politicians but was a diktat from the army.
"They don't want to leave any free voices in Sudan. ... Jan Pronk was the voice of those suffering in Darfur," he said.
Mr Pronk, 66, has been Secretary-General Kofi Annan's top envoy in Sudan for nearly two years. He was formerly the Dutch minister of environment and development cooperation.
Mr Pronk is known in Sudan for his dedication to his job but also his blunt comments, which irked some parties. Sudanese privately call him the "governor-general" of Khartoum, a reference to the former British colonial ruler.
Mr Ibrahim said although he had conflicts with Mr Pronk, he considered the UN official fair and unbiased.
"The government could not bribe him with money or contain him and that is why they want him out," he added.
Yasir Arman, a senior member of the ruling party's major partner in government, the former rebel Sudan People's Liberation Movement (SPLM), said it was wrong to expel Pronk and said the SPLM had not been consulted.
"It is a wrong decision which is going to worsen the situation of Darfur instead of solving it," he said. "It is another step towards the brink of confrontation with the international community."
Experts say 200,000 people have been killed and 2.5 million forced from their homes since mostly non-Arab rebels took up arms in early 2003 accusing the central government of neglect.
Pro-government militias are accused of a campaign of rape, murder and pillage, which Washington calls genocide.
Rebel commander Jar el-Naby told Reuters from North Darfur that militias had attacked again on Saturday about 100 km northwest of Darfur's main town of el-Fasher, raping two girls and looting villages.
Khartoum denies genocide but the International Criminal Court is investigating alleged war crimes in the region.
Only one of three negotiating rebel factions signed a May peace accord brokered by the African Union. Many non-signatories formed the new NRF alliance which renewed hostilities with the government in June.
Since the deal, violence has only escalated in Darfur, with rebel infighting and NRF clashes with the government. Tens of thousands more have been displaced and dozens of people killed.