But the security operation for the visit is being described as the biggest Israel has ever organised for a foreign dignitary.
Landing lights were smashed, the Vatican flag defaced and Nazi swastika symbols painted on the spot where the Pope will land on Tuesday during a week-long pilgrimage to Christianity's most sacred places.
An Israeli Government spokesman said the vandalism was a marginal act that would not disrupt the Pope's trip.
But the security operation for the visit is being described as the biggest Israel has ever organised for a foreign dignitary.
Extremist groups in Israel have expressed opposition to the visit and called for demonstrations while it is taking place.
Correspondents say some Israelis still resent the Vatican for its alleged lack of support for Jews persecuted by the Nazis during World War II.
Religious visit
The Pope last week apologised for persecution of Jews by Christians in the past, and has made a number of statements promoting reconciliation between the two faiths.
He insisted again on Sunday that his trip to the Holy Land is strictly religious, and called for prayers for the visit.
Speaking to 40,000 pilgrims in St Peter's Square, he asked Catholics around the world to pray for the success of what he called "an apostolic voyage so rich in significance".
His will be the first papal visit to the troubled region since 1964, fulfilling a dream of his 21 years as leader of the world's one billion Roman Catholics.
He said he would feel deep emotion as he visits places where Jesus lived and died.
Peace
But the 79-year-old Pope's trip is a gruelling one that will again test his health, worn down in recent years by advancing age and a host of ailments, including what is thought to be Parkinson's disease.
Lasting six days, it will take in Jordan, Israel and Palestinian-ruled areas following in the footsteps of Moses and Jesus.
As well as taking in holy sites, the pontiff will meet Palestinian leader Yasser Arafat and Israeli Prime Minister Ehud Barak, tour a Palestinian refugee camp and pay a visit to the Yad Vashem Holocaust memorial.
A key theme of the trip is how to improve relations among Judaism, Christianity and Islam, all of which consider Jerusalem a holy city.
"The Pope wants his journey to serve the cause of peace and contribute to bringing peace and justice to a region which has not known either," the Vatican's chief spokesman said last week.
The Pope arrives in Jordan on Monday.