The Syrian Ministry of Justice disclaimed the accusations, according to state-run news agency SANA. It called them part of an effort to harm the government's international reputation after recent victories over rebels.
The report contains damning allegations of torture followed by what Amnesty calls "sham trials," culminating in executions detainees likely did not see coming. Those who were released and left the country paint a grim picture that corroborates much of the report.
CNN spoke with two of those men, who said they were freed from prison and are now refugees in Sweden and Germany. CNN could not independently verify the details of the mens' accounts.
Omar al-Shogre, 21, said he was arrested in November 2012 simply for being a man named Omar from Baniyas, the site of intense sectarian clashes.
Later, jailers accused him of possessing anti-aircraft missiles. The allegations seemed to matter little in the indiscriminate torture he endured in military jails and police branches before arriving at Saydnaya in 2014.
Shebal Ibrahim, 39, was arrested in September 2011. He made one stop at al-Qaboun military police branch before he was transferred to Saydnaya in a meat truck.
Beatings upon arrival
Both men said they were beaten by soldiers as soon as they set foot in the red building, part of the Saydnaya Prison Complex, where the majority of civilian detainees were held. Another facility -- the white building -- was for military officers and soldier detainees.
Wooden sticks, cable cords, electric shocks and items resembling tank belts were used to subdue prisoners, al-Shogre said.
After the initial beating the soldiers stripped prisoners of identification, passports and money, before resuming the beatings.
But the worst was yet to come.
Forced to drink from a toilet
Detainees were crammed into cells with a single toilet that became their only source of nourishment on some days, they said.
Al-Shogre said he started out in a cell measuring two-and-a-half by two-and-a-half meters (8 feet by 8 feet) with 11 others. One day, prison officials cut the water entirely, causing people to hallucinate.
The next day, people started to drink urine. The following day some people died due to the lack of water, he said.
Ibrahim said he shared a one-by-two-meter (3.2 by 6.5 feet) cell with seven people. He remembers it was freezing inside.
He remembers sharing one piece of bread and a handful of olives among them.
He remembers drinking water from the toilet when they cut off the water one day.
There were two types of torture, Ibrahim said. "The torture for everyone and individual torturing," he told CNN.
"The daily routine was being tortured every day."
In addition to the collective torture of detainees in cells, Ibrahim said he was subjected to numerous beatings, even after he left Saydnaya for a hospital to treat a tumor in his liver.
"Everyone used to beat me there, including the nurses, doctors and the cleaning workers," he said.
After he returned to Saydnaya one of his cellmates died, maybe of kidney failure, maybe from the cold, he said.
When he called out that a man was in the cell the soldiers started to beat the detainees and the dead body, he said.
"They beat the dead body for two hours shouting 'You shouldn't die, you should be tortured more,'" he said.
The two men did not elaborate on specific details of torture. In Amnesty's last report on Syrian prisons
, detainees said jail officials pulled out their fingernails and toenails to extract confessions -- or, simply as punishment. Other detainees told Amnesty they were scalded with hot water, burned with cigarettes, even raped.
Sham trials: The difference between life and death
Ibrahim was lucky. He didn't end up in a hangman's noose like some 13,000 detainees Amnesty estimates met that fate.
The report says prisoners are moved in the middle of the night from their cells under the pretext of being transferred. They are taken to another building on the grounds of the prison, where they are hanged, likely unaware of their fate until they feel the noose around their neck, Amnesty alleges.
The report contends that the executed detainees were given a sham trial by "a so-called Military Field Court."
Ibrahim said he was taken from his cell one day and waited six hours for his hearing before the field court.
The session lasted just one minute, he said.
"The judge asked me silly questions, then he told me to 'f--k off,'" Ibrahim said.
Then, he was freed, he said. He provided CNN with a document signed by Col. Nasr Muhammad Shabani, the general attorney of the military court. The document said he was sentenced to 15 years of hard labor due to act of terrorism, but it also said that he should be freed immediately.
CNN could not independently verify the authenticity of the document.
It was only after he left Syria that he found out about the secret hangings, he said. He remembers people being removed from the cells and thinking they were being freed or transferred to a court.
Now, he knows they may have suffered a different fate.