Militias allied to the South Sudanese army have been allowed to rape women in lieu of wages while fighting rebels, a UN report says.
Investigators found that 1,300 women had been raped last year in oil-rich Unity State alone, it said.
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.
According to the UN report, militias operated under a “do what you can and take what you can” agreement that allowed them to rape and abduct women and girls as a form of payment.
They also raided cattle and stole personal property, it added.
The scale and type of sexual violence committed in South Sudan constitute some of the most horrendous human rights abuses 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 forces and allied militias 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.
“Dozens of people suffered a slow and agonising death at the hands of government forces that should have been protecting them,” said Lama Fakih from Amnesty.
“These unlawful killings must be investigated.”
The civil conflict erupted in December 2013 after Mr Kiir accused his sacked deputy, Riek Machar, of plotting a coup.
Mr Machar denied the allegation but then formed a rebel army to fight the government.
Tens of thousands have died and more than two million have been displaced since then.
Amid a threat of sanctions from the UN, the two sides signed a peace deal in August last year but are yet to form a transitional government of national unity.