Russia summoned the Israeli ambassador to demand an explanation for Israel’s air raids in Syria last week, Moscow has confirmed, as an Israeli drone was blamed for the targeted killing of a senior pro-Assad fighter in a second reported incident.

The summons, made on Friday, was confirmed by Russia’s foreign ministry which said the Israeli ambassador to Moscow, Gary Koren, had been asked to explain an exchange of fire with Syrian government forces in which anti-aircraft missiles were fired at Israeli jets.

According to Israel’s Channel 2, the Israeli strike hit close to Russian troops.

Russia’s deputy foreign minister, Mikhail Bogdanov, said Russia had “expressed concern”. The diplomatic intervention marks the first apparent fracture in the secretive deconfliction arrangement between the Russian president, Vladimir Putin, and Israeli prime minister, Benjamin Netanyahu, over where, when and who Israeli jets can strike in Syria.

Israeli fighter jets fired upon during Syria mission in clash with pro-Assad forces Read more

Israel had interpreted the arrangement as giving it a relatively free hand to attack warehouses and shipments of advanced weapons destined for Hezbollah, the Iranian-backed and pro-Bashar al-Assad Lebanese militant group. But Friday’s raid, reportedly by four Israeli jets which penetrated Syrian airspace, appears to have changed that dynamic after the interception of an SA-5 missile that flew into Israel forced it for the first time in the six-year Syrian civil war to acknowledge an attack.

Syria’s use of anti-aircraft missiles against the Israeli jets, however, suggested an increased confidence in the Assad regime, which has seen a number of similar air raids by Israel. Syria’s ambassador to the UN, Bashar al-Jaafari, on Sunday insisted the Syrian response was “in line with Israel’s terrorist operation” and had “changed the rules of the game”.

Facebook Twitter Pinterest Israel’s ambassador to Moscow, Gary Koren. Photograph: Mikhail Pochuyev/TASS

The sharp uptick in tensions on Israel’s northern border has resulted in increased rhetoric by senior Israeli political and military officials, with the hardline defence minister, Avigdor Lieberman, warning that Israel would not hesitate to “destroy” Syria’s air defence system if it fired on Israeli jets again.

Israel was also blamed on Sunday for a drone strike near the south-west Syrian town of Quneitra which killed a man, Yasser a-Sayyed, described as a leader of the pro-Assad Homeland Defence Forces militia.

Commenting on last week’s events, the Israeli military’s chief of staff, Gen Gadi Eisenkot, referred to the airstrike on Sunday.

“We are taking action to prevent the transfer of advanced weaponry to Hezbollah, and we will spare no effort to prevent that in the future. Hezbollah has been violating UN resolutions and is gearing for war,” he said.

Outside of the recent rhetoric, however, what has been fast emerging in recent months is that Israel may have badly misjudged the potential outcome of the Syrian war.

It had anticipated a conflict that would undermine the Assad regime, seriously wound Hezbollah and push back Iran’s attempts to expand its influence. But since Moscow’s intervention, Assad’s forces and Hezbollah have clawed back territory from rebel groups and Islamic State, creating conditions more conducive for Iran to supply weapons to the Lebanese militants.

Brig Gen Nitzan Nuriel, a former director of counter-terrorism in the Israeli prime minister’s bureau, said conflict with Hezbollah was inevitable as the group sought ever more advanced anti-aircraft missiles, heavy rockets and tactical weapons, but he believed Assad had seriously misread the situation.

“Assad has not read the map correctly,” he said. “He believes it is only a question of weeks or months before he can declare a full victory and is looking to the next stage. I believe he is mistaken and that clashes in Syria will stay with us for the next three to six years.”

Discussing Russia’s role in Syria, he added more controversially: “Russia got the messages it needs to receive from Israel.” That was, he said: “Israel will not allow anyone, including Russia to get in the way of implementing our military mission.”