Dieter Graumann, secretary general of the Central Council of Jews in Germany, also said Jews were hurt by his support for an ultra-traditionalist Catholic group they consider bigoted against Jews, Muslims, gays, women and Protestants.
The close friendship that has developed between Christians and Jews "must put up with others saying things that hurt," he told Reuters after he and other Jewish leaders met the pope and Catholic prelates for about 25 minutes.
"A possible beatification of Pius XII would hurt us," said Graumann, referring to efforts to put the late pope on the path to sainthood. "For us he is the pope who kept his silence too coldly and loudly during the Holocaust."
Critics accuse Pius of not speaking up to defend Jews against the Nazis, but his defenders - including Benedict - say he did the best he could to help them. Graumann said the pope did not react to his objection to beatifying Pius.
Despite these differences, the Jewish leader stressed that the closed-door meeting was friendly and moving for him.
"This is an impulse for new closeness, for a deeper and even better relationship," he said.
Pope Benedict was in Berlin on the first day of his third and most difficult papal visit to his homeland. He met the Jews in the Reichstag building after addressing parliament there.
Hitler 'a pagan idol'
In his remarks to the Jews, Benedict said Christians should never forget the horrors of the Holocaust and should become increasingly aware of their faith's deep affinity with Judiasm.
Noting that the Nazis planned and organised the attempt to exterminate the Jews from offices in Berlin, Benedict called the city a "central place of remembrance."
Benedict, who as a teenager was forcibly enrolled in the Hitler Youth, said "only a few" Germans were able to see the contempt for humanity the Nazis displayed on Kristallnacht in 1938 when they burnt synagogues and Jewish stores.
Adolf Hitler, he said, was a "pagan idol who wanted to take the place of the Biblical God" and that the concentration camps showed what man is capable of doing when he rejects God.
The Society of Saint Pius X (SSPX), the rebel group the pope readmitted to the Church by lifting the excommunications against its four bishops, includes one bishop who has publicly denied the Holocaust.
Its members reject the Second Vatican Council, which gave up centuries of official Church anti-Semitism and stressed the shared roots of Judaism and Christianity, and the principle of religious freedom it defended.
The Jewish community in the German capital has expanded in the past 20 years from about 20,000 at the time the Berlin Wall opened to about 100,000 today. Much of that growth came from immigrants from Eastern Europe.
Elan Steinberg, vice-president of the American Gathering of Holocaust Survivors and their Descendants, welcomed the pope's meeting with German Jewish leaders and his reaffirmation of the importance of a continuing dialogue between the faiths.
"Above all, however, was the emotionally moving and landmark denunciation by this German-born pope of Hitler and the criminal Nazi regime in the heart of Berlin," he said in a statement. "We only wish it had been said some six decades ago
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