Shimon Peres has called for Iran and Israel not to live as enemies even as a website linked to Mahmoud Ahmadinejad's regime called for "the final annihilation of Israel".
The Israeli president and Nobel laureate, at a speech marking the creation of the Knesset 63 years ago, said that the two countries "were not born enemies".
"There is no need to live as enemies," said Mr Peres. "Do not allow the flags of hostility to cast a dark shadow over your historic heritage."
Addressing the Iranian people, he added: "Your people are a sensitive people that aspire for friendship and peace, and not for conflicts and wars."
But his comments came as a document by one of Iranian Supreme Leader Ayatollah Khamenei's strategists was published on the Alef website.
The article called for Iran to attack Israel by 2014 and also described the Jewish state as "a cancerous tumour for the Middle East".