"I know that you share my concern over the alarming decline in the Christian population in the Middle East, including Israel, through emigration," the pontiff said.
"I pray that ... ways will be found of reassuring the Christian community, so that they can experience the hope of a secure and peaceful future in their ancestral homelands."
The pontiff made the comments in an address to receive Israel's new ambassador to the Holy See, Mordechay Lewy, who became the fifth envoy since the Vatican and Israel established diplomatic relations in 1994.
He also called for Israel to allow greater mobility for Palestinians, including travel to places of worship, "so that they too can enjoy greater peace and security".
The pope said Palestinians had an equal right to prosperity and asked Israel "to make every effort to alleviate the hardship suffered by the Palestinian community".
"I do realize that the difficulties experienced by Christians in the Holy Land are also related to the continuing tensions between Jewish and Palestinian communities," he said.
Lewy said Israel would pursue all avenues toward peace, and assured the pope it was working to assist Christian communities. "We shall do our utmost to help strengthen the Christian communities in Israel as their essential presence in the Holy Land is deeply rooted and historically self-understood," Lewy said, according to the text of his address.
"Only when these issues are overcome will the Church be able to carry out freely her religious, moral, educational and charitable works in the land where she came to birth," he said.
The Pope has standing invitations from Israeli and Palestinian authorities to visit. Benedict's predecessor Pope John Paul II made a historic trip to the Holy Land in 2000.
The Associated Press and Reuters contributed to this report