Raisi's election "makes clear Iran's true malign intentions, and should prompt grave concern among the international community", foreign ministry spokesman Lior Haiat wrote on Twitter.
Iran has "elected its most extremist president to date", he said following Friday's vote. Raisi is "committed to Iran's rapidly advancing military nuclear program".
Israel fiercely opposes the 2015 nuclear deal between Tehran and world powers that offered its arch-foe Iran sanctions relief in exchange for curbs on its nuclear programme.
It argues the deal, from which US President Donald Trump withdrew three years later, could enable the Islamic republic to develop nuclear arms.
Iran has always denied seeking a nuclear weapon.
Raisi, an ultraconservative cleric, is set to take over at a critical time as Iran seeks to salvage the tattered deal and free itself from punishing US sanctions.
Israel's newly sworn-in Prime Minister Naftali Bennett has called efforts to revive the deal a "mistake that will give one of the darkest regimes legitimacy".
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