The SPLM-IO insurgents loyal to former vice president Riek Machar said they freed prisoners from the jail in Kajo-Keji early on Monday around 100km south of the capital Juba.
The government said the rebels had raided the prison, freed a number of people it described as prisoners-of-war, then left.
"It is lies created by the rebels that they have killed and captured people," government army spokesman Santo Domic Chol said.
The United Nations says at least 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.
Many people in and around Kajo-Keji have fled to Uganda to escape the fighting.
Women and children wait to be treated at a Medecins Sans Frontieres (MSF) support clinic in Thaker, Southern Unity, South Sudan
South Sudanese rebels said they had taken control of a town on the Ugandan border and killed 14 soldiers in the fighting, an account dismissed on Tuesday as "ridiculous and unfounded" by the government.
