Israeli airstrikes on Syrian targets overnight have triggered the most visible skirmish between the two neighbours since Syria’s civil war began in 2011, according to media reports.

Israeli warplanes were on a mission to destroy a weapons convoy destined for the Iranian-backed Lebanese militant group Hezbollah, reported Chicago Tribune citing Israeli officials.

Confirming the attack, the Israeli military said its aircraft struck several targets in Syria and were back in Israeli-controlled airspace when several anti-aircraft missiles were launched from Syria toward the Israeli jets.

Syria used Russian-made SA-5 surface-to-air missiles and Israel responded with its new anti-ballistic Arrow system, the Haaretz newspaper reported.

The exchange indicates that tensions may be escalating between the two countries as Syrian forces loyal to President Bashar Al Assad tighten their grip after years of civil war.

That could make it harder for Israel to prevent weapons being smuggled from Syria to the militant group Hezbollah in neighbouring Lebanon, reported Bloomberg.

The missiles triggered Israel’s emergency sirens, which may have forced the army to issue a rare communique confirming the skirmish. “At no point was the safety of Israeli civilians or the IAF aircraft compromised,” it said.

Israeli aerial defense systems intercepted one of the missiles, the army said, without elaborating. It would not say whether any other missiles struck Israeli-held territory, but said the safety of Israeli civilians and Israeli aircraft was "not compromised."

Israel is widely believed to have carried out several airstrikes in recent years on advanced weapons systems in Syria - including Russian-made anti-aircraft missiles and Iranian-made missiles - as well as Hezbollah positions, reported the Chicago Tribune.

It rarely comments on such operations and the military statement detailing the raid and comments confirming the operation by Israeli Prime Minister Benjamin Netanyahu were highly unusual.

"Our policy is very consistent. When we identify attempts to transfer advanced weapons to the Hezbollah, and we have the intelligence and the operational capability, we act to prevent that. That is what was and that is what will be," Netanyahu said.

Hezbollah is fighting alongside President Bashar Assad in the brutal Syrian civil war. The Iran-backed group is sworn to Israel's destruction and fought a month-long war with the Jewish state in 2006, stated the Chicago Tribune.

Syrian state television later said an Israeli jet was hit, a claim Israel denied.

It isn’t the first time that Syria has fired anti-aircraft missiles at Israel, but it was the first time that Israel officially deployed the Arrow system, Haaretz said.