The Commission on Human Rights in South Sudan said it had reasonable grounds to believe a county commissioner in the northern oil-rich state of Unity orchestrated gang rapes at a military camp.
The documented abuses also involved beheadings, with rape victims being forced to carry the severed heads, victims being burnt alive, and days of brutal sexual assaults, the UN experts said in a statement.
"Conflict-related rape and sexual violence in Unity State has become so systematic and is a direct result of impunity," said commission member Barney Afako.
Multiple witnesses said the Unity official planned and ordered the attacks, which were led by his deputy and followed strikingly similar patterns in different areas, according to the statement.
Investigators say sexual abuse has been used as a weapon by all sides in South Sudan's civil conflict, which erupted in 2013 and triggered Africa's biggest refugee crisis since the 1994 Rwandan genocide.
Michael Makuei, South Sudan's information minister and government spokesperson, dismissed the commission's statement as a fabrication.
"They come and sit in hotels here in Juba and fabricate these false reports on South Sudan to make a living ... I am saying these are false reports fabricated against the government," he told Reuters.