"It is unacceptable that a president of the international community would pronounce those words," he told public Radio Nacional de Espana.
"I have asked our political director to summon the Iranian ambassador to express our total and absolute rejection of these statements," he added.
Spain has "good relations" with Iran but "the response (to these statements) must be firm, categorical and unambiguous on the part of a country like Spain, the European Union and the international community," Moratinos said.
Iranian President Mahmoud Ahmadinejad launched a new verbal attack on Israel on Sunday, saying last year’s war between Israel and Lebanese militant group Hezbollah had started a "countdown" that will end with Lebanese and Palestinian militants destroying the Jewish state.
The Iranian president sparked outrage abroad shortly after coming to power in 2005 for saying that Israel should be "wiped from the map" and then repeatedly predicting that the state would disappear.
Last week Spain hosted talks between Iran’s top nuclear negotiator Ali Larijani and EU foreign policy chief Javier Solana on the Islamic country’s nuclear program.