Speaking to reporters after a brief meeting with the pope at the Church of Beatitudes in northern Israel, Barak said the pope's visit "contributed greatly to understanding the message of fraternity and tolerance between human beings and between nations."
In that, he added, the pope contributed to a better atmosphere in the peace process.
Barak said he had asked the pope to try and uncover the fate of Israeli soldiers missing since the 1982 Lebanon War, and an Israeli navigator Ron Arad, who was captured alive in Lebanon and disappeared.
He said he believed the pope's "international and moral standing will make it possible to act."
A spokesperson for Barak said the pope raised the issue of Christian Maronites who lived in the villages of Ikrit and Birem near the Lebanese border some 50 years ago, during Israel's War of Independence. Israeli troops had asked the villagers to leave temporarily, but since then successive Israeli governments have refused to let them return.
Supporters of the Maronites carried banners at Friday's papal Mass demanding their return. The prime minister's spokesperson and a spokesman for the Latin (Catholic) Patriarchate in Israel said they did not know Barak's response. In recent weeks a team of Israeli ministers has been seeking a solution.
The papal meeting with Barak was brief because the pope reportedly showed up late, and Barak had to get to his wife's family in Tiberias, not far from the Mass site, before the Jewish Sabbath began so as not to risk angering his Orthodox Jewish government coalition partners.