Heavy rains and flooding affected 22 districts in eight states in Sudan over the Eid al-Fitr holidays, the SUNA news agency reported on Saturday. The capital, Khartoum, was among the inundated areas.
At least 184 people were injured and some 6,100 families were displaced, many of whom were from North Kordofan and Nile states.
High winds and rain hit Sudan last week as people were marking the end of the holy month of Ramadan.
Kabi Jeremiah, the humanitarian attache at the South Sudanese embassy, said some 3,000 inhabitants of Jaborona, located near Khartoum, were among those affected by the flooding.
Shelters housing thousands of South Sudanese in the region were also destroyed by the flooding, and residents tried to move their belongings to areas not hit by flooding.
The Khartoum region experienced heavy floods in August 2013, with the UN saying at the time that at least 50 people were killed and more than 180,000 people were affected.