Ali al-Sadig, spokesman for the Sudanese foreign ministry, said that Pronk had been told to leave because of statements the UN envoy had written on his website.
Sunday's move follows accusations by the country's general command last week that Pronk, UN chief Kofi Annan's personal representative in Sudan, was "openly intruding in the armed forces' affair".
The Sudanese military said in a statement that it considers the envoy's presence and movements in Sudan "a military threat that adversely affects the performance of the armed forces" and declared him "persona non grata".
It also complained that the envoy had travelled around Sudan without government permission and dealt with rebel groups fighting the military in the western region of Darfur.
Pronk's spokeswoman refused to comment on the move, while UN officials in New York were not available to discuss the issue.
Sudan's foreign ministry had said that Pronk made "unacceptable" comments in his personal internet weblog about battles between Sudanese troops and rebels in Darfur, state television reported.
Pronk, a former Dutch diplomat, wrote on October 14 that government forces had lost "two major battles" in Darfur where they have been fighting the region's ethnic African population.
The Darfur conflict has displaced
more than two million people
"Losses seem to have been very high. Reports speak about hundreds of casualties in each of the two battles, many wounded soldiers and many taken as prisoner," Pronk wrote.
"The morale in the government army in north Darfur has gone down. Some generals have been sacked; soldiers have refused fighting."
The military said the remarks amounted to "psychological warfare on the armed forces by propagating erroneous information that casts doubts about the capability of the armed forces in maintaining security and defending the country".
About 200,000 people have been killed and around two and a half million have been forced from their homes in two years of revolt in Darfur.
Pro-government militias are accused of war crimes against the region's Christian and animist population.