A Sudanese health ministry spokesman denied the existence of cholera, calling the cases "groundless".
Cholera, a water-borne disease, is contracted by drinking and eating contaminated substances and causes severe diarrhoea and vomiting. It can be fatal if untreated within 24 hours.
The rains inundating many regions of Sudan for more than a month have caused 64 deaths and affected nearly 500,000 people, according to the United Nations. Tens of thousands of homes have been destroyed.
In order to prevent the epidemic, OCHA, the UN office for the coordination of humanitarian affairs distributed chlorine tablets to disinfect water for some 500,000 people.
OCHA estimates the rains will continue until mid-September.