"We are relieved to report that the 16 humanitarian aid workers, who had been detained by the Sudan Liberation Movement/Army (SLM/A), were released today," said the statement released in Khartoum.
The SLA has said it took the workers for their own protection because they had wandered into rebel-held territory.
"The group includes workers from UN agencies, non-governmental organisatons, and donors," the statement said.
At least 10,000 people are believed to have died and an estimated one million people have fled the impoverished region following attacks by government troops and the militias, with more than 100,000 of them taking refuge in neighbouring Chad, according to UN figures.
Sunday's UN statement added the workers had returned to their base in al Fashir, the capital of Northern Darfur state.
The UN agency for refugees says many of the 158,000 refugees encamped in neighbouring Chad are at risk of attack by militias, with malnutrition and disease spreading.
Humanitarian fears now focus on the failure to plant crops before the impending rainy season, with some agencies predicting mass starvation in the region.