The attacks on Friday came as aid workers tried to register refugees for food rations, the agencies said.
Registration had come into effect at the request of refugees who said some of those claiming aid were not bona fide recipients.
World Food Programme (WFP) spokeswoman Christiane Berthiaume said camp dwellers had pushed for the registration because outsiders sometimes come to the temporary settlements to try to get a share of the food for displaced people.
About 200 aid workers, from UN agencies including the United Nations High Commissioner for Refugees (UNHCR), the United Nations Children's Fund (UNICEF) and the WFP, were trying to register 100,000 people in eight camps around El Geneina.
"They were attacked with sticks and stones. At least eight people were wounded," Berthiaume told a news briefing in Geneva.
One aid worker was hospitalised with minor injuries.
Berthiaume said that some local leaders are believed to have encouraged the attacks but that aid groups did not know why they had been targeted.
Aid workers pulled out
Ron Redmond, spokesman of the UNHCR, said troops from the African Union were escorting the workers and their damaged vehicles back to El Geneina, capital of West Darfur.
"Some minor injuries have been reported as well as damage to vehicles," Redmond told reporters.
"Some minor injuries have been reported as well as damage to vehicles"
spokesman of the UNHCR
The UNHCR, WFP and other aid groups pulled staff out the camps after the beatings, he said.
"We'll have to see what the security situation looks like before continuing the registration," he added.
The region holds 60,000 to 70,000 of the two million people driven from their homes since rebels took up arms against Khartoum in early 2003.