"The biggest danger there, apart from the destruction we have seen of the world heritage sites ... is the illicit archaeological excavations," UNESCO general director Irina Bokova said.
She did not say whether those involved in such excavations had any alignment with Syrian President Bashar al-Assad or rebels seeking to oust him.
"Anybody can do it," she said.
Ms Bokova did not disclose details of the locations of the illicit excavations in Syria. In September UNESCO issued what it called a "red list" of types of artefacts to alert museums, collectors and auction-houses what to be on the lookout for from Syria.
Ms Bokova said illicit Syrian artefacts have surfaced in neighbouring Jordan.
In February, Maamoun Abdulkarim - head of Syria's antiquities and museums - said illegal archaeological digs have threatened tombs in the desert town of Palmyra and the Bronze Age settlement of Ebla.