"They were attacked with sticks and stones. At least eight people were wounded," World Food Programme (WFP) spokeswoman Christiane Berthiaume told a news briefing in Geneva.
One aid worker was hospitalised with minor injuries.
Ron Redmond, spokesman of the U.N. High Commissioner for Refugees (UNHCR), said troops from the African Union were escorting the workers and their damaged vehicles back to El Geneina, capital of West Darfur.
"My understanding is that some of the sheikhs or leaders in the camp actually urged these groups of youth to do this," he said, adding reports were still sketchy.
About 200 aid workers, from U.N. agencies including WFP, UNHCR and UNICEF, were trying to register some 100,000 people in eight camps around El Geneina.
The region holds an estimated 60,000 to 70,000 of the 2 million people driven from their homes since rebels took up arms in early 2003. The rebels accuse the Sudanese government of neglect and of arming Arab militia to loot and burn non-Arab villages, a claim which Khartoum denies.