The official said the deaths occurred when a torrential downpour struck the northern city of al-Dammer, the capital of River Nile State, on Tuesday, with the floodwaters surrounding five neighbourhoods and impeding access.
The rains also submerged parts of the main road between Atbara in northeastern Sudan and the capital Khartoum, about 300 kilometres (186 miles) to the south, cutting off traffic.
Sudan's rainy season reaches its height in August, typically affecting the south and southeast of the country. But in recent years, rainfall has increasingly reached into the desert regions to the north, and as far as the border with Egypt.
In the eastern state of Gedaref, authorities also reported roughly 600 homes were damaged in the rains and more than 8,500 acres of farmland left underwater.
Emergency officials in the state warned villages had been left isolated by the floods with key roads severed, particularly in the towns of Gallabat and Qala al-Nahl.
The area contains some of Sudan's most important agricultural zones, producing staples such as sorghum, sesame and groundnuts.
Sudan's meteorological authority issued an orange-level warning on Tuesday for Khartoum as well as the neighbouring River Nile and White Nile states.
It cited a "high risk" of further heavy rain, strong winds and thunderstorms likely to cause rapid water surges and flooding.
Sudan has been struck by flooding amid a devastating war between the army and the paramilitary Rapid Support Forces (RSF), now in its third year.
The conflict, which erupted in April 2023, has killed tens of thousands, displaced millions and ravaged vital infrastructure -- creating what the United Nations calls the world's largest displacement and hunger crisis.
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