"A UNAMID rescue team from El Geneina, West Darfur, found two peacekeepers alive while a search is ongoing to locate the other four," an official of the African Union-United Nations Mission (UNAMID) told AFP.
UNAMID did not release the nationality of the troops involved.
The six were swept away "by a powerful current" while escorting the World Food Programme (WFP) to Misterei, about 50 kilometres (30 miles) southwest of El Geneina, the West Darfur state capital near Chad, the official said requesting anonymity.
Floods across Sudan this month have killed about 50 people and affected more than 500,000, according to government figures.
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WFP spokeswoman Amor Almagro told AFP that the agency's five Sudanese and two foreign staffers are all safe.
They were going to monitor WFP projects in Misterei, where the organisation gives food assistance to about 10,900 people, she said.
In August last year three UNAMID peacekeepers from Tanzania drowned after their armoured vehicle became stranded while crossing a swollen river, UN Secretary General Ban Ki-moon reported to the Security Council last year.