The intervention came despite repeated concessions in the lead-up to the tour by the Vatican, which is desperate to smooth difficult relations with both the Jewish and Muslim worlds.

The Pope insists his eight-day trip is a "pilgrimage" to Holy Land sites but it has become embroiled in disputes over controversial comments he has made affecting relations with both religions.

Shortly before the Pope landed in the Jordanian capital Amman, where he was greeted by King Abdullah II and Queen Rania, a minister in the new Right-wing Israeli government of Benjamin Netanyahu released the text of a letter in which he referred indirectly to the Pope's lifting of the excommunication of Bishop Richard Williamson, the breakaway English Catholic bishop who has denied aspects of the Holocaust, in January.

"I would like to point out that Holocaust survivors in Israel and elsewhere sincerely hope that your excellency will clearly condemn the purveyors of Holocaust denial and antisemitism, some of whom profess loyalty to your Church," said the letter written by Yaakov Margi, Israel's religious affairs minister.

In contrast to his popular predecessor, John Paul II, feelings in Israel are ambiguous towards Pope Benedict, a German who had to join the Hitler Youth as a child during the war.

The Pope will visit the Yad Vashem Holocaust Memorial in Jerusalem on Monday, but he will not step inside the museum. He has backed the canonisation of the wartime pope, Pius XII, whose photograph in the museum is adorned with a caption accusing him of not doing enough to speak up for or help the Jews.

He has also spoken out on behalf of the beleaguered Palestinian Christian community, and presses for a two-state solution to the Palestinian issue.

Nevertheless, the Vatican has been at pains to concede to Israeli pressure over aspects of the visit.

After intense lobbying aides agreed the Pope would not make an address on a specially constructed stage in a Palestinian refugee camp that abuts the Israeli security barrier.

That platform would have provided television cameras with powerful images of him speaking against the wall, which cuts off Palestinian communities, and even of Israeli watchtowers in the background.

The address will be given inside, instead.

The Vatican also revoked an invitation to an audience with the Pope of an Arab-Israeli mayor who had condemned the invasion of Gaza, again after heavy pressure from the Israeli cabinet which called the mayor a "terror supporter".

After the row over Bishop Williamson, for which the Vatican again apologised, the bitterest divide remains that over Pope Pius. The Pope has put his beatification on hold, but has insisted Pius was a "great churchman".

Father Federico Lombardi, the Pope's spokesman, said the Vatican had already made its position on the Holocaust clear.

"I don't understand what we have still to say," he told The Daily Telegraph. "It is clear that the Pope condemns those who deny the Holocaust.

"He has already said many times that the Holocaust was a terrible crime."

Muslim groups meanwhile continue to attack the Pope over a speech he made in 2006 which quoted a Byzantine emperor who said the Prophet Mohammed had introduced "evil and inhuman" ideas into the world.

Jordan's Islamic Action Front say they "reject" and will boycott his visit, because he has not apologised clearly enough.

In his opening remarks at Amman airport the Pope said the visit gave him "a welcome opportunity to speak of my deep respect for the Muslim community".

He said: "It is my fervent hope and prayer that respect for the inalienable rights and dignity of every man and woman will come to be increasingly affirmed and defended, not only throughout the Middle East, but in every part of the world."

He is due to meet moderate Muslim leaders on Saturday.