The pope addressed several thousand Catholics attending an invitation-only mass at the site where the Bible says Jesus prayed the night before he was crucified, The Jerusalem Post reported.
"While understandable reasons lead many, especially the young, to emigrate, this decision brings in its wake a great cultural and spiritual impoverishment to the city," Benedict said.
Giovanna, a 16-year-old student at the Rosary Sisters School, said life is difficult in many ways. She said the security barrier erected by the Israeli government keeps her from visiting friends or going to religious ceremonies in the Old City.
The Christian population has dropped everywhere in the Middle East, The New York Times said. A century ago, about one-fifth of the region's population was Christian, but that has dropped to 5 percent.
Christians were once in the majority in Lebanon. In other countries, like Egypt, they had power and influence beyond their numbers, the report said.