An Israeli minister has said that by striking key Iranian sites in Syria, Israel sent a clear message to Iran that it would not tolerate an Iranian military foothold on its doorstep.

The wave of airstrikes came after Israel intercepted an Iranian drone that had infiltrated its airspace, and an Israeli F-16 was downed upon its return from Syria on Saturday.

It was Israel’s most serious engagement in neighbouring Syria since fighting there began in 2011 and the most devastating air assault on the country in decades.

The military said it destroyed the drone’s Iranian launching site along with four additional Iranian positions and eight Syrian sites, including the Syrian military’s main command and control bunker.

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The wreckage of a jet on fire near Harduf, northern Israel (Yehunda Pinto via AP)

The Syrian Observatory for Human Rights, which monitors the war in Syria through activists on the ground, said on Sunday that at least six Syrian troops and allied militiamen were killed in the airstrikes.

The six included Syrian troops as well as Syrian and non-Syrian allied troops, the Britain-based Observatory said.

Minister of Intelligence Israel Katz said: “They, and we, know what we hit and it will take them some time for them to digest, understand and ask how Israel knew how to hit those sites.”

He told Israel’s Army Radio: “These were concealed sites and we have intelligence agencies and the ability to know everything that is going on there and yesterday we proved that.”

In Saturday’s attacks, the Israeli jets came under heavy Syrian anti-aircraft fire and the pilots of one of the F-16s had to eject as the plane crashed in northern Israel. One pilot was seriously wounded and the other lightly.

Israel would not confirm whether its aircraft was shot down by enemy fire, which would mark the first such instance for Israel since 1982 during the first Lebanon war.

Israel has recently issued several stern warnings about the increased Iranian involvement along its borders with Syria and Lebanon, which it attributes to Iran’s growing confidence following Syrian president Bashar Assad’s successes in the civil war, thanks to support by main allies Russia and Iran.

Israel fears Iran could use Syrian territory to stage attacks or create a land corridor from Iran to Lebanon that could allow it to transfer weapons more easily to the Lebanese Hezbollah — an Iranian-backed Shiite militant group sworn to Israel’s destruction.

Hezbollah’s fighters are also fighting on Assad’s side in the Syrian civil war.

Though Israel has largely stayed out of the Syrian conflict, it has struck weapons convoys destined for Hezbollah dozens of times since 2012.

Israel has also shot down several drones that previously tried to infiltrate its territory from Syria, but the capture of an Iranian drone and the direct targeting of Iranian sites in response marked a dramatic escalation in the Israeli retaliation.

An F-16 plane crashed in northern Israel on Saturday (Rami Slush/AP)
An F-16 plane crashed in northern Israel on Saturday (Rami Slush/AP)

Prime Minister Benjamin Netanyahu has held several consultations with Russian president Vladimir Putin, who backs Assad’s government and maintains a large military presence in Syria.

Following the Israeli strikes they spoke again on Saturday, with Mr Netanyahu conveying Israel’s determination to counter Iran’s intentions.

Russia’s foreign ministry appeared to criticise Israel’s actions while the US strongly backed them.

“It is absolutely unacceptable to create threats to the lives and security of Russian servicemen who are in Syria at the invitation of its legitimate government,” the Russians said.

Heather Nauert, of the US State Department, said: “Iran’s calculated escalation of threat and its ambition to project its power and dominance places all the people of the region — from Yemen to Lebanon — at risk.

“The US continues to push back on the totality of Iran’s malign activities in the region and calls for an end to Iranian behaviour that threatens peace and stability.”