Syrian President Bashar al-Assad's Government has secretly executed between 5000 and 13,000 people in just one prison as part of its campaign to eliminate opposition to his rule, a new report by the watchdog group Amnesty International has found.

The killings took place over a four-year period between 2011 and 2015 in the notorious Sednaya facility outside Damascus, and the bodies were later disposed of in mass graves, according to the report released yesterday by Amnesty.

Human rights groups estimate that tens of thousands of political prisoners have disappeared in the Syrian prison system since the uprising against Assad's rule first erupted in 2011, and they suspect many of those have been tortured to death or secretly killed. The accounts of these killings are in addition to the figure of 17,000 that Amnesty counted in an earlier report on the extra-judicial killings issued in August last year, compounding an emerging picture of what Amnesty referred to as a policy of "extermination" against opponents of the Government.

The majority of those executed at Sednaya were political prisoners, including many of the ordinary people who joined in the peaceful protests against Assad, the report says. Some were rebels who took up arms and others were officers and soldiers who had defected from government forces. But for the most part they were "doctors, engineers, protesters", one former prison official is quoted as saying. "They were somehow understood to be linked to the revolution. Sednaya is the place to finish the revolutionaries. It's the end for them."

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The report describes in chilling detail how the prisoners were taken out of their cells in batches, of up to 50 at a time, twice a week and in the middle of the night, typically on Mondays and Wednesdays.

They were given only cursory trials lasting between one and three minutes at one of two military field courts that offered no semblance of judicial process, with sentences typically handed down on the basis of confessions extracted under torture. When the time comes for their execution, the prisoners are handcuffed, blindfolded and led to a basement cell containing 10 stands and 10 nooses.

A former judge from the military court described the executions, saying it would often take up to 10 to 15 minutes for the prisoners to die. "Some didn't die because they are light. For the young ones, their weight wouldn't kill them. The officers' assistants would pull them down and break their necks. Two officers' assistants were in charge of this."

Amnesty said it based its estimate of between 5000 and 13,000 hangings conducted in this way on testimony of 31 former prisoners, four prison officials and three judges familiar with specific instances of the executions and the frequency with which they appeared to occur. They are identified in the report only by their last names because of concerns for their safety.

Amnesty said the executions "amount to war crimes and crimes against humanity" and are authorised at the highest levels of the Syrian Government.

"The horrors depicted in this report reveal a hidden, monstrous campaign, authorised at the highest levels of the Syrian Government, aimed at crushing any form of dissent within the Syrian population," said Lynn Maalouf, deputy director for research at Amnesty International's regional office in Beirut.

The allegations come at a sensitive time for Assad, who is in the process of crushing the nearly 6-year-old rebellion against his rule but still lacks international legitimacy. The findings of the report should be on the agenda for the next round of Syrian peace talks, due to be held in Geneva on February 20, Amnesty said. It also called for an independent United Nations investigation into the atrocities.

The report also contains details of what it calls the "sadistic and dehumanising" conditions under which the prisoners are kept, including repeated torture and the systematic deprivation of food, water and medical care. Many more prisoners die from torture and neglect, Amnesty said.

"Many of the prisoners said they were raped or in some cases forced to rape other prisoners. Torture and beatings are used as a regular form of punishment and degradation, often leading to life-long damage, disability or even death," the report says.

"The cell floors are covered with blood and pus from prisoners' wounds. The bodies of dead detainees are collected by the prison guards each morning, around 9am."