It said yesterday that the Sudanese police had informed it that the suspect was arrested on Sunday.
Both the accused and the alleged victim of the incident in El Fasher, the capital of North Darfur state, are Sudanese nationals, it said.
"The mission condemns, in the strongest possible terms, any instance of sexual exploitation and sexual abuse committed by UN personnel in the Darfur region," mission chief Jeremiah Mamabolo said in a statement.
Being a civilian employee and a Sudanese national, the suspect does not have the full immunity enjoyed by expatriates working for the UN mission.
Sudanese officials claim that the conflict in Darfur has ended, but UN rights experts have regularly highlighted cases of rights abuses including rapes in camps for people displaced by the conflict.
War erupted in Darfur in 2003 when ethnic minority rebels mounted an insurgency against the Arab-dominated government of President Omar al-Bashir, which they accused of economic and political discrimination.
The joint African Union-United Nations Hybrid Operation in Darfur, also called UNAMID, was deployed in Darfur in 2007 to rein in the conflict.
It is currently undergoing a major downsizing of its peacekeeping force.
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