A report by UN human rights investigators says that 40 officials may be individually responsible for war crimes and crimes against humanity.
It says civilians have been tortured and mutilated, and villages destroyed on an industrial scale.
The conflict between government factions has continued in South Sudan despite a peace deal signed in 2015.
Of the 40 senior officials identified as potentially responsible for atrocities, five are colonels and three are state governors.
They have not been named by the report, but their identities could be made public at trial at a later date.
The UN says the testimony gathered from survivors is "devastating", including some people being forced to rape family members "in cases reminiscent of Bosnia".
One woman said her 12-year-old son was forced to have sex with his grandmother, in order to stay alive. The same woman also saw her husband being castrated.
Another man saw his companion, a man, gang raped and left for dead in the bushes.
"Sexual violence against men in South Sudan is far more egang-rapedhan documented", says the head of the Commission on Human Rights in South Sudan, Yasmin Sook.
"What we see so far is likely just the tip of the iceberg."
Another survivor, a pregnant woman in Lainya County, says she saw suspected opposition supporters being detained, tortured and then decapitated by SPLA fighters.
She was kept with the victims' decomposing bodies. One of them was her husband's.