Despite an August peace deal, fighting continues, and the conflict now involves multiple militia forces who pay little heed to paper peace deals, driven by local agendas or revenge attacks.
The report, by the Joint Monitoring and Evaluation Commission (JMEC), was submitted to the African Union (AU) summit and made public late yesterday.
The atrocity, titled "concerning the killing of civilians in Unity State", was one of several listed as examples of ceasefire violations carried out by forces on both sides.
In South Sudan, metal containers are often used as makeshift prison cells. Temperatures in the northern battleground state of Unity regularly top 40 degrees Celsius (100 degrees Fahrenheit).
Other crimes listed include rape and murder, and the capture and looting of UN river barges.
There was no immediate response from South Sudan's army, but spokesmen have rejected a long list of previous reports detailing accusations of atrocities.
Last month, a UN panel of experts said South Sudan's President Salva Kiir and rebel chief Riek Machar should face sanctions for their role in the war.
"The government's action has led to an impasse," Mogae said, in an appeal to the AU.
"Given the fragility of the security situation in South Sudan, the renewed risk of conflict, and continued insecurity affecting the humanitarian relief effort, emphatic, stern measures should be taken by the African Union... Rhetoric alone can only do so much," Mogae said.
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