Seated at the Kremlin, Prime Minister Benjamin Netanyahu and President Vladimir Putin smiled and shook hands. At a follow-up media briefing, the Israeli leader announced a deal to avoid hostilities between their militaries in and around Syria.

But all the pleasantries Monday couldn’t hide the awkwardness of the new wrinkle in Russian-Israeli relations. Moscow’s decision to boost its military presence in northern Syria in support of President Bashar al-Assad has posed a potential challenge to Mr. Netanyahu, who for years has had a relatively free hand to carry out strikes against arms shipments that Israel says goes from Iran, through Syria, to the Shiite militia Hezbollah in Lebanon.

If Israeli intelligence gets tipped off that Syrian forces are shipping advanced missiles to Hezbollah near where Russian troops are stationed, Netanyahu is liable to face a dilemma: should Israel attack the weapons convoy preemptively and risk injuring Russians? The coordination mechanism announced by Israel is supposed to avoid tactical “misunderstandings,” but potentially crimps Israel’s maneuvers.

“It complicates reality. It potentially limits Israel’s freedom of action,” said Ehud Eiran, a political science professor at Haifa University who focuses on national security. “The fascinating question is whether it will constrain Israel or not. Israel has been looking at Lebanon and Syria as areas where it could fly freely.”

Not since the collapse of the Soviet Union has Israel faced a potentially unfriendly superpower so close to its borders. Though Russia is no longer supporting a coalition of Arab states in direct conflict with the Jewish state as it did during the cold war, the fallout from the Russian intervention could boost the Iranian-led alliance of Shiite forces supporting Mr. Assad.

Speaking to Israeli reporters after the Kremlin meeting, Netanyahu said Israel would continue to act to block weapons transfers from Syria to Lebanon and against the establishment of an Iranian-backed military front on the Golan Heights.

Israel has intervened in Syria for years

Israel’s policy of intervening against perceived threats from Syria goes back to 2006, when it bombed a nuclear reactor there. While acknowledging Israeli concerns about spillover from the war, Mr. Putin played down Israeli fears of a new front in Syria, saying Russia’s actions would be “responsible.”

But that’s not the same as assuring Israel it can continue to operate freely in Syrian airspace, analysts say.

“In effect, Russia is dictating by saying, ‘Our soldiers, rockets, and aircraft are there. Don’t mess with us,’” says Moshe Maoz, an expert on Syria at Hebrew University. He sees the new dialogue with Russia as a strategic mistake for Israel.

“It’s going to advance the expansion of Iran. Israel can’t do very much about it, but Israel is shooting itself in the foot by agreeing” to the coordination with Moscow, he says. “Israel is undermining its relations with the Sunni Muslim majority” in Syria and the region by cooperating with an ally of Assad.

Russia filling a vacuum

Indeed, over the years of the Syrian civil war, Israeli policymakers have disagreed over whether they prefer the chaos that would come with the collapse of the Assad regime and the consequent strategic blow to Israel’s chief enemy in Iran, or the relative stability if the so-called “devil that it knows” remains in power.

Even though the Russians are filling a vacuum in Syria left by Israel’s chief ally, the United States, some security analysts in Israel wonder if Russia might help to tamp down arms shipments to Hezbollah.

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Eyal Zisser, a Syria expert at Tel Aviv University, says such assistance is unlikely, but he does believe the coordination will have a tactical benefit by avoiding a flare-up with Israel’s enemies active in Syria.

“The Russians are the only ones that speak with all the powers,” he says. “It’s important to keep the channels open, and avoid escalation.”