Children and the disabled in South Sudan have been burned alive and pro-government militia allowed to rape women as a form of payment, a new UN report has said.

The investigation accused all sides in the country's civil war of targeting civilians for murder and rape but said the army and government-allied forces were most to blame for what it described as "one of the most horrendous human rights situations in the world".

"The report contains harrowing accounts of civilians suspected of supporting the opposition, including children and the disabled, killed by being burned alive, suffocated in containers, shot, hanged from trees or cut to pieces," the UN human rights office said in a statement on Friday.

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More than 1,300 rape cases were recorded in just one of South Sudan's states - the oil-rich Unity state - over a five-month period last year, the report said.

WATCH: Women of South Sudan: Broken bodies, shattered dreams One woman told the UN investigators she had been stripped naked, raped by five soldiers in front of her children on the roadside, then raped again by more men in the bushes only to return and find her children missing.

"Credible sources indicate groups allied to the government are being allowed to rape women in lieu of wages but opposition groups and criminal gangs have also been preying on women and girls," the UN said.

The prevalence of rape "suggests its use in the conflict has become an acceptable practice by (government) SPLA soldiers and affiliated armed militias," it added.

South Sudan presidential spokesman, Ateny Wek Ateny, denied that government forces and allied groups had committed atrocities.

"As a responsible government we take every report seriously, when the report is about human rights violations. However, our forces are under strict command to observe human rights and to protect civilians," he told Al Jazeera.

"If there are individuals, soldiers, that comes to violate human rights, then they are doing it at their own peril because the government does not authorise anybody to kill civilians.

"We tell them .. to minimise civilian casualties when they are actually forced to fight."

READ MORE: Tens of thousands killed in South Sudan war, says UN

The UN report is the work of an assessment team deployed to South Sudan between October and January.

Al Jazeera's diplomatic editor James Bays, reporting from Geneva, said the UN human rights office has rarely released a report "as shocking and as damning" as the one published on Friday on South Sudan.

He added that the UN human rights chief Zeid Raad al-Hussein described South Sudan as a crisis that had fallen off the international radar.

Rupert Colville, a spokesperson for the UN Commissioner for Human Rights, said the report is probably "just the tip of the iceberg" as most of the fighting takes place in remote areas.

"It's a very difficult country to get around; there are no roads and it's a huge area and many small villages that have been affected," Colville told Al Jazeera.

He added that journalists, civil society activists and human rights workers trying to expose what is happening in the country have suffered threats and in some cases have been killed.

"One of the key issues is total impunity," Colville said. "Across the board you have really a dysfunctional system where people with power, people with guns, seem to be able to do whatever they want and know they are not going to get any comeback."

South Sudan descended into conflict in December 2013 after President Salva Kiir accused his former deputy Riek Machar, who he had sacked earlier that year, of plotting a coup.

The clashes that followed set off a cycle of retaliatory killings that have split the world's newest country, which won its independence from Sudan in 2011, along ethnic lines.

Tens of thousands have been killed and more than 2.3 million displaced.

The UN findings came as rights group Amnesty International released a separate report detailing how South Sudanese government soldiers killed more than 60 men and boys last October by locking them into a shipping container until they suffocated.