U.N. spokesman Martin Nesirky said the ambush on a United Nations-African Union peacekeeping patrol in El-Geneina took place Tuesday evening.
The U.N. Security Council late Wednesday condemned the attack "in the strongest terms" and called on all parties in Darfur to cooperate with the peacekeeping mission.
Nesirky said the secretary-general "is appalled and deeply saddened" by the latest attack on peacekeepers in Darfur.
The Security Council and the secretary-general urged Sudanese government to swiftly investigate the incident and bring the perpetrators to justice.
Darfur has been torn by conflict since 2003, when rebels took up arms against the central government, accusing it of discrimination and neglect. Violence has tapered off, but clashes continue and peacekeepers remain a target.