The human rights group says as many as 13,000 people have been executed at Saydnaya prison, north of the capital Damascus in a "hidden" campaign authorized by senior regime figures.
Amnesty's report, Human slaughterhouse,
says prisoners are moved in the middle of the night from their cells under the pretext of being transferred. They are taken to 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 Syrian Ministry of Justice disclaimed the accusations, calling them part of an effort to harm the government's international reputation after recent victories over rebels, according to state-run news agency SANA.
The report is the culmination of a yearlong investigation, including interviews with 84 witnesses including security guards, detainees, judges and lawyers, Amnesty says.
Most of those hanged were civilians "believed to be opposed to the government," the report finds.
"The horrors depicted in this report reveal a hidden, monstrous campaign, authorized at the highest levels of the Syrian government, aimed at crushing any form of dissent within the Syrian population," Lynn Maalouf, the deputy director for research at Amnesty's Beirut office, said in a statement announcing the report.
Amnesty International says there are two detention centers at Saydnaya prison. In the "red building," the majority of detainees are civilians who have been arrested since the beginning of the conflict in 2011, according to the organization. In the "white building," the detainees are mainly military officers and soldiers.
The report contends that the executed detainees were given a sham trial by "a so-called Military Field Court."
"The judge will ask the name of the detainee and whether he committed the crime. Whether the answer is yes or no, he will be convicted ... This court has no relation with the rule of law. This is not a court," a former judge said, according to Amnesty.
Nicolette Waldman, an Amnesty International researcher, elaborated on the horrific conditions prisoners allegedly face.
"They have been actually dying in massive numbers as a result of repeated torture in combination with the systematic deprivation of food, water, medicine and medical care," she told CNN.
"(The report) has gotten the attention it deserved," Waldman said. "It's a big story. But for people who work on Syria, it was almost a test case for 'Does the world still care, not just about death but the fact that it was organized, systematic?'"
In light of its findings, she said Amnesty is calling for investigation without delay and for the UN to act immediately.
"I want to be very clear that these practices are unacceptable, and they have to stop. They have to be brought to an end. Mass killings of civilians and extermination so that people are dying of starvation, of illness, of treatable diseases must stop, and Russia has a very special responsibility to uphold peace and security in the world," Waldman said.
"We are calling on them to use their influence with the Syrian authorities to push for access to independent monitors to all of the prisons in Syria run by the government where these atrocities are taking place so the perpetrators can be held to account."
Speaking at the UN, UK Ambassador and Deputy Permanent Representative Peter Wilson responded to the report's allegations.
"We have seen the report of Amnesty International on atrocities in Syria," he said. "Our foreign secretary has said he is sickened by that report. We strongly condemn these atrocities, and we continue to effort to shine a light on what's happening in Syria and to hold people accountable for these actions."
'Just a headline'
President Assad's regime has previously been accused of extrajudicial killings and war crimes during the country's civil war, which broke out in 2011.
, CNN was given a copy of a report that found "direct evidence" of "systematic torture and killing" by the Syrian government, based on photographs leaked by a Syrian defector.
One of the report's authors called it a "smoking gun" proving the use of torture.
But Assad has steadfastly maintained that many of the accusations leveled against him are politically motivated.
"I'm just a headline -- the bad president, the bad guy, who is killing the good guys," Assad told a group of western visitors, including The New York Times
, in November. "You know this narrative. The real reason is toppling the government. This government doesn't fit the criteria of the United States."
The UN estimates that about 400,000 people have been killed since the start of the war and another 4.8 million have fled the country.