Airline manager Gabriel Ngang confirmed the plane crash and says 45 people were on board, including five crew members.
An aircraft engineer at the Wau airport, Paul Charles, said the plane tried to land in bad weather Monday and hit a damaged truck on the side of the runway. "The pilot couldn't control it", said Youngule, who is also deputy director of Air Traffic Services.
"The weather was not good", Achieng said, citing very cloudy conditions.
The fate of the 44 passengers are not known, with no official statements made.
The passenger plane was coming from the capital Juba.
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On social media, images appeared of the plane with smoke billowing from the wrecked fuselage.
South Supreme Airlines is a South Sudanese airline which began operations in September 2013, Airlive said.
Ateny Wek Ateny, the South Sudanese presidential spokesperson, was quoted as saying: "It is miraculous, completely".
One official told Agence France Presse at least 14 people survived the crash, while a radio station in Juba reported nine people had been pulled out alive and rushed to hospital.