A walnut tree stripped of its branches stands in the rubble of the Kalat al-Numan citadel, originally built during the Roman era some 2,000 years ago. (John Cantlie/AFP/Getty Images)

Syria’s vast archaeological sites have suffered extensive damage because of bombing by government warplanes and the demolition of religious shrines by Islamic State militants. But there is an increasing, perhaps more menacing problem: old-fashioned plunder.

A new report has found evidence of “widespread looting” at locations that Syria has nominated as UNESCO World Heritage Sites.

Under threat are the remains of a Mesopotamian trading post and a 4,500-year-old city that housed thousands of cuneiform tablets, as well as an ancient town with a chapel known for containing the world’s oldest depictions of Jesus, according to the report, released this past week by the American Association for the Advancement of Science.

[View: Satellite images show Syria’s damaged World heritage sites]

Susan Wolfinbarger, director of the association’s Geospatial Technologies and Human Rights Project, which produced the study, said in a statement that “unlike our previous analysis of Syria’s World Heritage Sites, we’re seeing a lot of damage that appears to be the result of widespread looting.”

A member of Syria's government forces gestures near the partially destroyed entrance of Aleppo's historical citadel on Sept. 4, 2012. (Joseph Eid/AFP/Getty Images)

The report draws on satellite imagery of six of the 12 sites that Syria has nominated for World Heritage status.

Four of those have sustained extensive damage, according to the findings, which were compiled with help from the University of Pennsylvania Museum’s Penn Cultural Heritage Center and the Smithsonian Institution.

Three of the damaged sites suffer from looting that “appears to have ramped up during the last year,” the report states, citing images of what look like excavation vehicles and thousands of pits where impromptu digging seems to have taken place.

The study, which will be followed by a report on damage to the country’s other six proposed World Heritage sites, identifies Dura-Europos, a city with roots in the 3rd century B.C., as the most affected by looting. On the west bank of the Euphrates River, it was influenced by the ancient Greeks as well as Romans and Persians, and it houses a well-preserved synagogue and an ancient chapel with paintings of Jesus thought to be produced in A.D. 235.

The report adds to evidence that the level of looting iafter nearly four years of fighting “is virtually unprecedented” in modern history, said Michael Danti, an archaeology professor at Boston University. He also is the co-director of the American Schools of Oriental Research Syrian Heritage Initiative, which is funded by the State Department to monitor at-risk sites in the country.

Six locations in Syria have already received World Heritage status, and most of them have been badly damaged amid fighting between government forces and rebels. Perhaps the most well known is Aleppo, where parts of the Great Mosque and the citadel have been smashed.

“The level of destruction of archaeological sites in Syria since the uprising began has been catastrophic,” said Charles E. Jones, an expert on Middle East antiquities at Pennsylvania State University. Given that so many areas of the country contain ancient artifacts, he said, it is “hardly surprising that this has happened as the chaos has deepened.”

The new study found that damage to one proposed World Heritage site, the eastern city of Raqqa, probably did not result from fighting or looting. The city, founded in 300 B.C., is the capital of the Islamic State’s self-declared caliphate, which spans territory in Syria and Iraq. During medieval times, Raqqa briefly served as the capital of an Islamic empire that stretched from central Asia to North Africa.

The destruction of structures in the city was likely due to demolitions by the Islamic State, also know as ISIS or ISIL, the report says.

The Islamic State has destroyed historical treasures in Iraq and Syria, including churches, mosques and religious shrines, that do not fall in line with its rigid interpretation of Sunni Islam.

The group also has profited from stealing and selling artifacts. In Iraq, it reportedly controls over 4,000 archaeological sites.

Desperate for cash, ordinary Syrians also have participated in looting, and so have forces loyal to the regime of Syrian President Bashar al-Assad. Smuggling rings spirit away the items to Europe and other areas.

Pascal Butterlin, a professor of archaeology at the University of Paris who has spent 20 years working in Syria, wrote in an e-mail that the looting of the country’s archaeological sites was the “worst patrimonial disaster since World War II.”

Correction: An earlier version of this story gave an incorrect title for Susan Wolfinbarger. She is director of the Geospatial Technologies and Human Rights Project.