BERLIN — By day, the workers used heavy machinery to dig pits and trenches. After dark, the corpses arrived, sometimes hundreds at a time, in the beds of military pickups or in refrigerator trucks meant for transporting food.

As government intelligence officers looked on, the dead were dumped into the ground and buried near the capital, Damascus, according to men who worked at two mass grave sites in Syria. Sometimes, the workers packed the dirt down tightly to keep dogs from digging up the bodies.

Throughout Syria’s 11-year civil war, human rights groups and government defectors have documented the widespread killing of civilians by the security forces as they sought to stamp out any opposition to the dictatorship of Bashar al-Assad.

Now, The New York Times has gathered evidence that sheds new light on one enduring mystery of the war: What happened to the bodies of the many thousands who died or were killed in government detention centers?

Interviews over the past several months with four Syrian men who worked at or near secret mass graves led to an examination of satellite images. Together, those clues revealed the locations of two sites. Each one holds thousands of bodies, according to the men who worked there. They could also contain powerful evidence of war crimes committed by Mr. al-Assad’s forces, according to human rights groups, including the systematic torture and the killing of detainees.

“If the issue of the missing and the disappeared is not resolved, there can never be peace in Syria,” said Diab Serrih, the co-founder of an association of former detainees in Syria’s notorious Saydnaya prison that has worked to locate mass graves. “Every day, we get calls from people who want to know where their sons are,” he added. Many of them say, “‘I just want to see a grave so that I can put a flower on it.’”

After the uprising that led to the war began in 2011, Mr. al-Assad activated his network of security agencies to stamp out dissent by locking up protesters, activists and others.

At least 14,000 of those detainees were tortured to death, the U.S. Treasury Department said last year, but the actual number is almost certainly much higher. More than 130,000 others have disappeared into government detention centers, and many of them are presumed dead.

The Syrian government has repeatedly denied that it killed people in detention. But human rights groups have extensively documented the practice. One important body of evidence came from a Syrian police photographer, code named “Caesar,” who fled the country in 2013 with images of more than 6,000 dead bodies, some bearing signs of torture.

Counting and identifying the bodies in the mass graves would only be possible by digging them up. But that is unlikely to happen as long as Mr. al-Assad remains in power. Russia, his strongest backer, continues to support him, and he and his senior officials have never been held accountable for atrocities such as the use of chemical weapons against their own citizens.

To draw attention to those atrocities, the Syrian Emergency Task Force, an advocacy group, brought one of the men interviewed by The New York Times to Washington this week to speak with members of Congress and others about the mass graves.

Many of the bodies of those who died in detention were sent to government hospitals, where their deaths were recorded, according to reports by Human Rights Watch and others. The four men interviewed described what happened next.

All four worked on or near mass graves near Damascus and each saw parts of the government’s efforts to dispose of bodies. Two of the men are now refugees in Germany, one is in Lebanon and one remains in Syria. Three spoke on condition of anonymity for fear of retribution by the Syrian government.

The Times could not independently corroborate all the details in their accounts, including the total numbers of bodies they recalled seeing. And they each saw only part of the government’s burial operations, which human rights groups say were likely replicated in other mass grave sites across the country.

One of the men interviewed testified about what he witnessed at a landmark trial in Germany about war crimes in Syria that concluded this year with a life sentence for a former Syrian intelligence official convicted of crimes against humanity.

He said he had worked before the war for the Damascus regional government overseeing civilian burials. In mid-2011, intelligence officers recruited him to dispose of corpses coming through hospitals from detention centers, he said. He did this work for six years at the two mass grave sites.

The first mass grave site his team worked at, from mid-2011 until early 2013, was in a civilian cemetery in Najha, a town south of Damascus, he said. At first, he oversaw a few laborers who buried small numbers of bodies, he said. But as the conflict grew more violent, the numbers increased and he became what he described as a cog in a vast bureaucracy of death.

He was given a white Nissan bus adorned with photos of Mr. al-Assad, a military uniform and a permit that allowed him to cross checkpoints, he said. Before dawn, he would drive more than a dozen workers to the mass graves.

Separately, large refrigerator trucks meant to transport food brought the corpses from the hospitals to the graves, he said. When they arrived, his team would dump the bodies in the ground. Many of the bodies had bruises, lesions and missing fingernails, he said, and some were decomposing — indicating it had been some time since their deaths.

He did not bury the bodies himself, he said, but oversaw the workers and received papers from the hospitals saying how many bodies had come from each detention facility. He recorded those numbers in a logbook in his office, but left those papers behind when he fled Syria in 2017, he said.

At some points during the six years he worked at the mass graves, his team unloaded two trucks about twice per week, each carrying anywhere from 150 to as many as 600 bodies, he said. The team also received a few dozen bodies per week from Saydnaya prison, which Amnesty International once branded “a human slaughterhouse,” where torture was rampant and prisoners were often killed.

The bodies that came from Saydnaya often appeared to be recent deaths, he said, adding that some had what looked like rope marks around their necks or gunshot wounds. Sometimes, they dumped the bodies in trenches and covered them with dirt. At other times, they stacked up to eight bodies in graves meant for a single body, he said.

Satellite images of the Najha cemetery during that period show graves filling up, and one image from 2012 shows a truck with its rear pointed toward the graves and a white vehicle nearby, possibly a bus.

During the trial in Germany for the former Syrian intelligence officer convicted of crimes again humanity, two other people also testified about mass graves in Najha.

One of them was Eyad al-Gharib, a former Syrian official convicted last year of complicity in crimes against humanity for driving arrested protesters to a security office known for torture. He told the court that dead detainees were buried in Najha if their bodies showed signs of torture.

Another man interviewed by The New York Times was a bulldozer driver who worked in the Najha cemetery for seven months in 2012. He said intelligence officers overseeing the burials told him to dig large square pits.

He, too, described refrigerator trucks arriving a few times per week throughout the time he worked there, carrying hundreds of bodies each time that the workers dumped into the ground. He covered them with dirt, he said, sometimes rolling his bulldozer over the site to pack it down tightly to prevent dogs from digging up the bodies.

He recalled the smell of death being so strong that it made him faint.

Once, he said, seven bodies, including two women and a child, arrived in an ice cream truck. The sight still haunts him a decade later in Germany, where he is a refugee.

“I can no longer eat ice cream,” he said.

In early 2013, the man who drove the white bus said the government started a new mass grave near a Syrian army base in Qutayfa, a town north of Damascus.

There, a motorized excavator dug trenches up to 100 yards long, he said. When the refrigerator trucks arrived, they inclined their beds to dump the bodies in one end of the trench. If they got stuck, the workers dragged them into the trench, where the excavator buried them.

The next group of bodies went in the next part of the trench, a grueling process that was repeated until the trench was full, he said. Then, the excavator would dig a new trench.

Based on his accounts, The New York Times located the site and examined satellite images from that period that showed long trenches that were gradually filled with dirt. Some images show an excavator at the site, and at least one shows a white bus.

Walid Hashim, a former soldier who served in Qutayfa before defecting at the end of 2012, identified the same location as a mass grave. In a phone interview, he said the site was a shooting range that the government dug up to bury the bodies of people who had died in custody.

The area was closely guarded to keep people away, he said, but everyone on the base knew what it was for.

“You didn’t talk about it or ask about it,” Mr. Hashim said. “But everyone who worked there knew about the graveyard.”

Christoph Koettl contributed reporting from New York, Karam Shoumali from Berlin and Asmaa al-Omar from Beirut.