"Twenty-two districts in eight states were affected by flooding and heavy rain," the Sudan News Agency (SUNA) news agency reported, citing the federal health ministry.
There were 184 injuries during the deluge which affected around 6,100 families, about half of them in Nile and North Kordofan states, SUNA said.
Homes in the capital Khartoum were also inundated when rain and high winds lashed the region last Tuesday night and on July 25 at the start of the rainy season.
Shelters housing South Sudanese there have been destroyed, he told AFP on Thursday.
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"That one is washed away," he said.
Residents tried to move their meagre belongings to dry ground while they manually dug out channels to drain the water, Jeremiah added.
Thousands of impoverished South Sudanese have been living in rough shelters in Jaborona and numerous other outdoor settlements in the Khartoum area.
They have been waiting in vain for assistance to travel to South Sudan after the country's independence three years ago.