Chad's military has accused rebel groups based in Darfur of trying to topple the government of Chadian President Idriss Deby and of staging raids from their base from within Sudan.
The United Nations will not evacuate all staff, its chief spokesman Stephane Dujarric said, according to a Reuters report.
"Essential life-saving humanitarian services delivered by the U.N. will continue, and the mission will monitor the situation and carry out a fresh security assessment of the area in the next two to three weeks," Dujarric said.
The move, according to U.N. special representative in Sudan Jan Pronk, follows "increased instability in the affected areas, including a buildup of forces on either side of the [Sudan-Chad] border, with increased potential for armed conflict."
"The decision taken will result in a considerable reduction in the presence of U.N. staff and restricted U.N. access in the affected areas," Pronk said in a U.N. report.
Some 11,000 aid workers currently work in Darfur, undertaking one of the world's largest humanitarian operations and combating what U.N. Secretary-General Kofi Annan has called one of the world's worst humanitarian crises.
The crisis is the result of an ongoing battle between Sudan's Arab-dominated government and mostly-black African rebels in Darfur angered by what they see as the government's failure to provide resources for their region.
Tens of thousands of civilians in Darfur have died in the violence.
In response to a rebel uprising in March 2003, the Khartoum government is accused of unleashing armed bands of Arab militiamen, who have carried out attacks, including rape, looting and murder, on Darfur villagers. The attacks have forced more than 2 million Darfurians into displacement camps in Sudan and Chad.