The employees of two foreign and one national organisation disappeared during clashes between government and rebel forces in the Bahr el-Ghazal region, with both sides accusing the other of having attacked the aid workers.
Government officials said rebels aligned with former vice-president Riek Machar had kidnapped the workers during clashes, while the rebels said they had "rescued" the workers from government forces.
One of the NGOs, France-based Solidarites International, said its three workers had been "retrieved Wednesday" and were "out of danger", but did not give further details on what had transpired.
The NGOs were working on issues of food security in the country which is faced with a severe humanitarian crisis after four years of war.
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The region in which the aid workers went missing has been the centre of fierce fighting between the government and rebel forces since 2016.
In April three people delivering food aid were brutally killed in the second largest city of Wau, a sign of the difficulties for humanitarian workers in dealing with the fallout from a conflict which has killed tens of thousands and driven nearly four million from their homes.
South Sudan's leaders fought for decades for independence, but once they got it in 2011, a power struggle between President Salva Kiir and his former deputy Riek Machar led to all out civil war in 2013.
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