"Iran is putting in great efforts to fortify its presence in Syria. This is a threat for Israel, for the Middle East and, I believe, for the whole world," Netanyahu said in remarks translated into Russian posted on the Kremlin's website.
"Iran has furthered its control and influence on Iraq, on Yemen. In practice, it in many ways has real control over Lebanon," he said as the two met in Russia's Black Sea resort of Sochi.
"We cannot forget for a minute that Iran continues to threaten to destroy Israel on a daily basis," Netanyahu said, accusing Tehran of "arming terrorist organisations."
Putin supports the regime of Bashar al-Assad, which is also strongly backed by Iran.
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Since Syria's civil war erupted in 2011, Israel has maintained a policy of attacking arms convoys intended for its Lebanese arch-foe Hezbollah, which backs the Syrian regime and fought a devastating war against the Jewish state in 2006.
Israel seized 1,200 square kilometres (460 square miles) of the Golan Heights from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the international community.
Around 510 sq. Km. Remain under Syrian control.
Israel and Iran regularly accuse each other of being a threat to stability in the region.