The Syrian government is carrying out an extermination policy among its prisoners that has resulted in thousands the deaths, UN rights investigators said Monday in Geneva, accusing the country's leadership of crimes against humanity.

Islamic State extremists had also committed crimes against humanity by killing and torturing prisoners, the investigators of the Commission of Inquiry on Syria said in a new report.

Anti-government rebels and al-Nusra Front, al-Qaeda's Syrian branch, were responsible for killing detainees, but these war crimes were not carried out in a widespread and systematic manner, according to the findings.

"Civilian superiors at the highest levels of government (...) have knowledge of the crimes or allegations of crimes being committed by their subordinates" or have consciously disregarded such information, the human rights investigators said.

They called on the UN Security Council to adopt sanctions against those responsible, and to launch proceedings at the International Criminal Court in The Hague or at a special tribunal.

"As soon as the Security Council would decide on a referral to justice, it would be great because we could give all our evidence to this judicial institution," said Commission of Inquiry member Carla del Ponte, a former UN war crimes prosecutor.

The new report came during a pause in UN-brokered peace talks by government and rebel representatives, which are scheduled to resume on February 25 in Geneva.

"We are persuaded that [there can be] no peace without justice," del Ponte told reporters.

Since the conflict started in March 2011, Syrian authorities have rounded up civilians across the country who are suspected of supporting the opposition or of being disloyal to the government of Bashar al-Assad.

Tens of thousands of people are being held by the government at any given time, said the panel, chaired by Brazilian legal expert Paulo Sergio Pinheiro.

The human rights experts were not allowed into Syria, but they interviewed more than 600 people for their report, including some 200 former prisoners who saw fellow inmates die.

The report said many had died from torture, such as one man who had his genitals mutilated in 2014 during an interrogation in a centre operated by the 4th division of the army. He was left bleeding and died three days later from his untreated injuries.

A large number of inmates died from lack of hygiene, food, drinkable water or medical care.

"Many prisoners were forced to use their toilet as a source of drinking water," the report said.

Witnesses also told the UN experts of rampant rape and sexual violence, and of the fatal psychological toll of such inhumane treatment.

"Numerous accounts describe how some detainees started hallucinating or displaying other signs of psychological disorders, stopped eating and drinking, and eventually passed away in their cell for unidentified reasons," the UN experts wrote.

While most of the victims have been men, the UN commission documented cases of women and children as young as seven dying in prison.

"The killings and deaths described in this report occurred with high frequency, over a long period of time and in multiple locations, with significant logistical support involving vast state resources," the commission said.

Commission chairman Paulo Sergio Pinheiro said the Syrian government officials had rejected all accusations of human rights violations, without offering any clarification.

"Blunt denial is not sufficient," he said.

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