The Sudanese government has said the UN cannot move new troops to its tense North-South border without its consent.
It comes after the UN's peacekeeping chief said troops would be sent to "hotspots" at the request of the semi-autonomous South's president.
There is growing tension in the country in the run-up to a referendum on Southern independence due to be held in January, correspondents say.
The referendum was part of a 2005 peace deal that ended the civil war.
On Friday, UN peacekeeping chief Alain Le Roy said the UN force would increase its presence along the 2,000km (1,250 mile) border.
He said the increase would be limited to "hotspots" and that the UN could not create a full "buffer zone" between the regions.
Officials at the UN said the decision had been made following an appeal from South Sudanese President Salva Kiir, who was concerned the North was preparing for war.
But President Omar Hassan al-Bashir's security adviser, Salah Gosh, rejected the plan, saying troops could not be deployed without the consent of the government.
Ibrahim Ghandour, another leading politician in Mr Bashir's National Congress Party (NCP), said any tension in the region could be sorted out between the two sides, so a buffer zone between North and South was not necessary.
The BBC's James Copnall in Khartoum says there has been a surge in inflammatory statements in recent weeks in Sudan, as the referendum approaches.
There is also a huge argument about who can vote in a second referendum, in which the oil-producing region of Abyei will decide on whether to join the North or the South, our correspondent adds.
Sudan is divided between the mainly Muslim and Arab-speaking North, and the South, where most people are Christian or follow traditional religions.
Many in Sudan are concerned the ongoing tensions around the referendum will see the country return to civil war.
The last North-South conflict lasted two decades and left two million people dead.