The rains have washed out roads and prevented vital supplies from reaching towns and rural areas, the Sudan Tribune reported.
A vehicle carrying 12 people was washed off the road Monday night at a bridge crossing over the Luri River, said Charles Barnaba Kisanga, minister of information and communications for Western Equatoria State. All the passengers were believed to have died.
In Lakes State, three people including a 9-year-old child died due to flooding. More than 2,000 people were forced from their homes when the Gel River overflowed, said Awerial County commissioner David Mayom Riak.
Kisanga said the government had been unable to maintain the roads because of austerity measures introduced after South Sudan stopped oil production in January in a dispute with neighboring Sudan.
South Sudan gained independence from Sudan last year.