"Drainage systems are unreliable, and stagnant water in different locations create conducive conditions for water-borne and vector-borne diseases such as cholera, dengue fever, rift valley fever, and chikungunya, in a country with an extremely fragile health system," it said.
Heavy rains usually fall in Sudan from June to October, and the country faces severe flooding every year.
Officials have said they had recorded the highest waters on the Blue Nile - which joins the White Nile in the Sudanese capital Khartoum - since records began over a century ago.
The rising Nile floodwaters also threatened to swamp the ancient archaeological site of Al-Bajrawiya, once a royal city of the two-millenia-old Meroitic empire.
The area includes the famous Meroe pyramids, a UNESCO World Heritage site.