But in televised remarks following the talks, Netanyahu did not mention the Palestinian issue, focusing instead on Iran.
"I asked him, as a moral figure, to make his voice heard loud and continuously against the declarations coming from Iran of their intention to destroy Israel," Netanyahu said of his talks with the pope.
"I told him it cannot be that at the beginning of the 21st century, there is a state which says it is going to destroy the Jewish state, and there is no aggressive voice being heard condemning this," the Israeli leader told Israel TV.
He said Benedict said "he condemns all such things, anti-Semitism, hate," adding: "I think we found in him an attentive ear."
While President Mahmoud Ahmadinejad of Iran has called for Israel's elimination, his exact remarks have been disputed, with some translators saying he called for Israel to be "wiped off the map." Others say a better translation would be "vanish from the pages of time" - implying Israel would disappear on its own rather than be destroyed.
Since taking office on March 31, Netanyahu has emphasized the Iranian threat in an apparent attempt to put the Palestinian question on the back burner.
Unlike previous governments, Netanyahu's has refused to endorse the two-state formula, potentially putting him on a collision course with President Obama. The two will meet in Washington next week.
The Israeli leader called his meeting with Benedict "very good and important," noting that the pope heads a church of 1 billion followers, and Israel wants good relations with them.
"Secondly, we spoke also about the historic process of reconciliation between Christianity and Judaism, and the pope is very interested," Netanyahu said.
