Militias allied to the South Sudanese army have been allowed to rape women in lieu of wages during fighting against rebel forces, a UN report says.
Investigators found that 1,300 women were raped last year in the oil-rich Unity state alone, it added.
In a separate report, Amnesty International says more than 60 men and boys were suffocated in a shipping container by government forces.
The government denies its army targeted civilians but says it is investigating.
"We have rules of engagement and we are following them," a spokesman for President Salva Kiir, Ateny Wek Ateny, told the BBC's Newsday programme.
The scale and type of sexual violence committed in South Sudan is the most horrendous human rights abuse in the world, UN High Commissioner for Human Rights Zeid Ra'ad Al Hussein said.
One woman said she had watched her 15-year-old daughter being raped by 10 soldiers after her husband was killed.
The UN said government fighters abducted and gang-raped girls, and cut civilians to pieces. It also accused opposition fighters of committing human rights abuses.
Researchers from Amnesty International said bodies of those suffocated were dumped in a field after they were killed last October in Leer Town, Unity State.
Thousands of people have been killed and millions displaced since 2013.
"Dozens of people suffered a slow and agonising death at the hands of government forces that should have been protecting them. These unlawful killings must be investigated," said Lama Fakih from Amnesty.
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