"Heavy rains and floods in Sudan have affected lives and properties of some 65,957 families or 320,000 people," it said in a bulletin on Wednesday.
The Khartoum region has been particularly hard hit, the WHO added .
As of Wednesday, 48 people had been killed in the flooding and 70 injured.
One of the major health concerns is the collapse of 52,856 latrines that pose "serious risks" to public health.
"This is a huge disaster," Mark Cutts, who heads the UN's Office for the Coordination of Humanitarian Affairs in Sudan, said last week.
He said the UN is ready to support the government to help those affected by the floods, even though UN humanitarian operations in Sudan "have been severely underfunded" in 2013.
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