Pope Benedict XVI walked out of an inter-faith meeting in Israel last night after a Palestinian cleric called on the pontiff to help stop Israeli "crimes".

The Pope is visiting some of the holiest sites in Judaism and Islam today in the latest stage of his Holy Land pilgrimage.

The Vatican has insisted the trip is a spiritual, not political journey, but that has not stopped Palestinians from looking to him to criticise Israeli restrictions on their freedom of movement and the ongoing occupation of Palestinian territory.

At one point, the Catholic leader – who has dedicated his visit to reconciliation between the three mutually distrustful religions - walked out of an interfaith meeting last night when a Palestinian Muslim cleric attacked Israeli policy in Jerusalem, and called on the Pope to help stop Israeli “crimes”.

Israel’s Chief Rabbinate announced it was boycotting the forum until the cleric was banned from it.

But the call for Papal intercession was repeated again this morning when Benedict visited the Dome of the Rock, Islam’s third holiest site built atop the vast stone platform that once housed the Jewish Temple, Judaism’s own holy of holies.

Mohammed Hussein, the Grand Mufti of Jerusalem, urged his visitor to work to end Israeli “aggression” against Palestinians.

“We look forward for your holiness’s effective role in putting an end to the ongoing aggression against our people, our land, and our holy sites in Jerusalem, Gaza and the West Bank,” he said.

The Pope is due to visit a Palestinian refugee camp tomorrow as the residents – whose forebears were driven from their homes in what became Israel during the 1948 Arab-Israeli war – prepare to mark Naqba, or Catastrophe, Day, known to Israelis as Independence Day.

Fending off various attempts to drag him into the Israeli-Palestinian conflict, the Pope has striven to fill his speeches with neutral, religious references to peace, justice and security, and called for reconciliation between all faiths in a city divided by religious and nationalist enmity.

“Here the path of the world’s three great monotheistic religions meet, reminding us what they share in common,” the Pope said as he became the first holder of the office to visit the Dome of the Rock shrine, from where Muslims believe Mohammed ascended to heaven to meet previous prophets.

“This sacred place serves as a stimulus, and also challenges men and women of goodwill to work to overcome misunderstandings and conflicts of the past and set out on the path of a sincere dialogue,” he said.

More recently the mosque compound, which overlooks the Western Wall – a holy site to Jews – has served as a lightning rod for nationalist tensions. A visit to the compound in 2000 by Ariel Sharon, the Israeli general who went on to become prime minister, marked the start of the Second Palestinian Intifada in which thousands of people died.

The Pope also prayed silently for several minutes at the Western Wall, for centuries the only part of the former Temple where Jews were allowed to pray. In keeping with the traditions of the place, he left a paper note for God, which the Vatican said bore the message: “Send your peace upon this Holy Land, upon the Middle East, upon the entire human family.”

While the Pope turned to God for deliverance from violence, Israeli security forces used more earthly measures to ensure his safety at the flashpoint holy sites: snipers scoured the buildings nearby for possible attackers and helicopters droned overhead. Israel has deployed some 80,000 security personnel to protect its high-profile visitor.

The Pope was due to head later to Mass in the Garden of Gethsemane, just outside the Old City walls, where Jesus is said to have had the Last Supper and been betrayed by Judas.