The 19-seater commercial Baby Air plane had been travelling from the capital, Juba, the minister of information for the town of Yirol, Taban Abel Aguek, told The Associated Press.
Officials are investigating the cause of the crash.
The three survivors are a six-year-old child, an adult man and an Italian doctor with an aid organisation who was in surgery and in serious condition, Mr Aguek said.
"There were people everywhere," the minister said of the crash site.
Yirol is in the central part of the civil war-torn East African country.