"Prime Minister [Benjamin] Netanyahu told President [Vladimir] Putin that this move will only increase Iran's aggression in the region and undermine stability in the Middle East," the Israeli government's press service said in a statement.
In response, the Russian leader reassured Netanyahu lifting the embargo on the advanced ground-to-air missile systems' delivery to Iran would not threaten Israeli security.
"Putin stressed that the S-300 missile system is purely defensive and will not pose a threat to Israel or any other country in the Middle East," the Kremlin press service said in a statement.
Two weeks after six major powers reached a landmark provisional agreement with Iran on its nuclear program, Putin signed a decree allowing the resumption of Russia's contract with Iran.
Three years later, a UN Security Council resolution banning countries from providing arms to Iran, including missile systems, forced former President Dmitry Medvedev to suspend the system's delivery.
Netanyahu had previously lobbied the five permanent UN Security Council members and Germany, known as the P5+1, not to go ahead with the Iranian nuclear deal, which is still subject to finalization by the end of June. Tel Aviv maintains that easing restrictions against Tehran threatens regional security.
The United States, a close Israeli ally, expressed concern with Russia's S-300 deal with Iran, but reiterated the P5+1 group's unity in ongoing talks over the Islamic republic's contested nuclear program.