The Prime Minister's Office said Netanyahu told the Russian president that putting advanced weapons systems in irresponsible hands would increase dangers in the region. Netanyahu added that Israel will continue to protect its security and interests.
Netanyahu also reiterated Israel's position that Syria was responsible for the downing of a Russian military plane last week, which killed 15 Russian airmen. The prime minister added that Iran also bore responsibility as it was destabilizing the area.
Russia, however, "proceeds from the premise that the actions of the Israeli Air Force were the main cause of the tragedy," the Kremlin said in a statement after Putin's phone call with Netanyahu.
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Putin told Netanyahu that supplying the surface-to-air missile system to the Assad regime is "intended to thwart any potential threat to the lives of the Russian military service members fulfilling the tasks of combatting international terrorism," the Kremlin said.
Israel's security cabinet is set to convene Tuesday morning to discuss the diplomatic crisis with Russia ahead of Netanyahu's departure to attend the UN General Assembly session in New York.
Russia announced earlier Monday that it will supply the S-300 missile system to Syria in two weeks against strong Israeli objections, a week after Moscow blamed Israel for indirectly causing the downing of the plane.
Russian newspaper Kommersant quoted a senior official in the Russian defense ministry, who posited that the deployment of S-300 in Syria would severely hamstring the Israel Air Force.
U.S. National Security Adviser John Bolton responded to the development, saying that Russia's actions would constitute a "significant escalation" by Moscow, adding that he hopes the Kremlin will reconsider.
Kremlin spokesman Dmitry Peskov said Russia's decision to supply Syria with the S-300 system is aimed at increasing safety of Russian military. When asked about relations with Israel, Peskov said the decision was not directed at any third country.
Russian Defense Minister Sergei Shoigu said on Sunday that Russia would go ahead with the shipment because "the situation has changed, and it's not our fault." He also said that Russia would start to electronically jam aircraft flying in to attack targets in Syria. "We are convinced that these measures will calm down some hotheads and keep them from careless actions which pose a threat to our troops," Shoigu said.