Pope Benedict, on his first visit to Israel, said the suffering of six million Jews murdered by Nazi Germany in the Holocaust must never be denied or forgotten.
In a gesture addressing Jewish anger over his lifting of the excommunication of a Holocaust-denying bishop in January, the pontiff went to the Yad Vashem Holocaust memorial to honour the dead and meet survivors of the concentration camps.
He spoke of the "horrific tragedy of the Shoah", the Hebrew term for the Holocaust, and called it an atrocity that had disgraced mankind and must never be repeated.
The chairman of Yad Vashem council, Rabbi Israel Meir Lau, expressed disappointment that the Pope was not more explicit.
"There certainly was no apology expressed here," he said. There was no "expression of empathy with the sorrow".
The pope made a moving speech, Rabbi Lau said, but "something was missing. There was no mention of the Germans or the Nazis who participated in the butchery, nor a word of regret."
In the 45 years since the Second Vatican Council repudiated the concept of collective Jewish guilt for Christ's death, relations between the Vatican and the Jewish state have been haunted by the church's actions during the Holocaust.
Ties plummeted to a low in January when Pope Benedict lifted the excommunication of British Bishop Richard Williamson, who denied six million Jews were killed.
In a conciliatory message later, he told Jewish leaders that "any denial or minimisation of this terrible crime is intolerable".
Speaking on his arrival from Jordan, the pope condemned anti-Semitism, which he said "continues to rear its ugly head" in the world, and called for a global effort to combat it.
He also called for a "just resolution" of the Israeli-Palestinian conflict "so that both peoples may live in peace in a homeland of their own, within secure and internationally recognised borders".
The call highlighted political differences with Israel's new, right-leaning government. Since becoming prime minister six weeks ago, Benjamin Netanyahu has not endorsed creation of a Palestinian state, a US and Arab priority, and instead puts Israel's security first.
Using a Hebrew word, the pope said security is something that "arises from trust and refers not just to the absence of threat but also to the sentiment of calmness and confidence".