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One report says some of the six bodies found beside a road outside the western town of Yambio were handcuffed and blindfolded. The report cites local residents as saying South Sudanese government troops carried out the killings "on the premise that they were suspected rebels".
The UN officials also found burned huts near the bodies and estimated the killings were in early December.
The deputy spokesperson for South Sudan's army, Santo Domic Chol, says civilians frequently accuse the military of abuses and have a "political agenda".
The discovery of the bodies comes shortly after the UN officials warned of increasing ethnic violence in South Sudan's civil war.
