The Sudanese Professionals' Association said on Tuesday that rains over the weekend have caused floods that destroyed or damaged more than 1,300 homes on the southern outskirts of the city, where the White and Blue Nile rivers meet.
The SPA says the flooding could lead to epidemic diseases and overwhelm sanitation services.
Footage circulated online showed flood waters cutting off roads and sweeping away houses and people's belongings. Large swathes of agricultural land in the area have been flooded.
Military rulers have deployed troops to help people deal with the flooding. The Health Ministry has said at least 12 province have been affected by torrential rains since earlier this month.
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