A war monitor has reported that the Jordanian air force launched deadly strikes in Syria in January and December as Amman pursues efforts to fight drug smuggling.
Amman has not confirmed it carried out the raids, although it had previously vowed to fight the narcotics trade in cooperation with war-torn Syria.
In Damascus's first comments on the strikes, the foreign ministry said: "Syria deeply regrets Jordanian Air Force strikes on... Syrian territory."
"There is no justification for such military operations," it said.
Jordan's foreign ministry lashed back at Syria, describing drug and arms smuggling across the border from the country as a "threat to national security".
"Jordan will continue to confront this danger and anyone standing behind it," it added in a statement.
One of the main drugs smuggled out of Syria is the amphetamine-like stimulant captagon, for which there is huge demand in the oil-rich Gulf.
Captagon is by far Syria's biggest export, dwarfing all its legal exports put together, according to estimates drawn from official data by AFP.
Talks between Jordanian Foreign Minister Ayman Safadi and Syrian President Bashar al-Assad established a forum to combat drug smuggling from Syria, which held its first meeting in Amman in July.
But Jordan's strikes were not consistent with what was agreed on by both sides, the Syrian foreign ministry said.
Damascus "has expressed its readiness to cooperate with Jordanian civil and security institutions, but those messages were ignored," it added.
Jordanian foreign ministry spokesperson Sufyan Qudah said the kingdom had provided Syria during those meetings with a list of smugglers, drug factories, storage facilities and smuggling routes in government-controlled areas.
"Yet no real measure has been taken to neutralise this risk, in fact smuggling attempts have seen a dangerous increase," Qudah said, adding that Amman was still ready to cooperate with Damascus to halt arms and drug trafficking.
Fighting drug trafficking from Syria was one of the main issues that drove regional re-engagement with Assad's government, which was re-admitted to the Arab League in May after more than a decade of isolation.
Since 2011, Syria has endured a bloody conflict that has claimed more than half a million lives and displaced several million people.
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