ISIL fighters moved from northeast Lebanon to Syria as part of deal with Hezbollah and Syrian government forces.
Israeli fighter jets have struck a military facility in western Syria, killing two people, according to a Syrian commander quoted by the state-run news agency SANA.
The army statement said the air strike caused material damage near the town of Masyaf and warned against the “dangerous repercussions of this aggressive action to the security and stability of the region”.
The air raid was carried out from Lebanese airspace and two people were killed at the site, SANA said, adding that it would embolden “terrorists” in Syria fighting the government.
“Israeli warplanes at 2:42am today fired a number of missiles from Lebanese airspace, targeting one of our military positions near Masyaf, which led to material damage and the deaths of two members of the site,” the Syrian army said in a statement.
Al Jazeera’s Mohammed Jamjoom, reporting from Beirut in Lebanon, said that while the Israeli government had not commented, Lebanese local media outlets were reporting they saw Israeli warplanes breach Lebanese airspace and that the sound barrier was broken over Lebanon in the skies at around 2:30am local time (11:30 GMT).
An Israeli army spokesperson declined to discuss reports of the air raid, saying the army did not comment on operational matters.
However, Yaakov Amidror, a former head of the country’s National Security Council, told Israel’s Army Radio on Thursday that the air raid would be an effort to weaken Iran and Hezbollah, the Lebanese armed group, which operates in Syria.
“We do not interfere in the question of who will rule in Damascus; we interfere with the question of how strong Iran and Hezbollah will be in the region,” Amidror said.
Our correspondent said that while the Israeli government rarely discusses military activity regarding Syria, it has in the past got involved in “worrying about the proliferation of chemical weapons”.
“More often, they have commented on the fact that they have tried to prevent weapon shipments going from Iran and getting to Hezbollah bases here inside Lebanon, or to Lebanese fighters who are fighting alongside the Syrian government and troops inside of Syria,” he said.
Masyaf is a town in Hama province in western Syria, approximately 60km east of the coastal city of Tartus, where Russia maintains a naval base.
The UK-based Syrian Observatory for Human Rights (SOHR) said the site targeted by Israel is home to a research centre sanctioned by the US as part of Syria’s non-conventional weapons agency.
An AFP news agency report said Syria’s army operates a military facility north of Masyaf that includes a training camp and a branch of the Scientific Studies and Research Center (SSRC).
On Wednesday, UN war crimes investigators announced they had an “extensive body of information” indicating Syrian warplanes were behind the attack.
Syria’s army did not mention the SSRC in its statement. The government has rejected accusations of chemical weapons use in Khan Sheikhoun as “fabrications”.