The government said the rebels raided the prison, freed a number of people it described as prisoners-of-war, then left.
South Sudan's civil war has displaced about 2.5 million people and created a devastating humanitarian crisis
The SPLM-IO insurgents loyal to former vice president Riek Machar said they freed prisoners from the jail in Kajo-Keji on Monday around 100km south of Juba.
"It is lies created by the rebels that they have killed and captured people,’’ government army spokesman Santo Chol said.
The UN says no less than a quarter of South Sudan’s population has been displaced in a three-year civil war triggered by President Salva Kiir’s decision to sack Machar in 2013.
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However, many people in and around Kajo-Keji have fled to Uganda to escape the fighting.
