Thousands also lost their homes in Northern Bahr el Ghazal State after the mostly mud constructions disintegrated in high waters, the region's acting governor Arkangelo Athian told Reuters.
"Some were killed when their houses collapsed on them at night, others sank in the river when they were trying to cross to high land," Athian said.
"They are sleeping on the roads," he said, adding that the flooding continued.
A U.N. spokesman said officials were planning to visit the area on Wednesday to make an emergency assessment.
The low-lying land also flooded in July, affecting at least 39,000 people, most of them recently returned refugees.
Thousands have returned to the area after a 2005 peace deal ended a north-south war that was fuelled by religion, ideology and access to oil.
