Her rare and public demand came amid increasing outrage among Germany's Roman Catholic leaders over the pope's decision to lift the excommunication of British-born Richard Williamson, who questioned whether 6 million Jews were gassed during the Nazi Holocaust.
Merkel said she "does not believe" there has been adequate clarification of the Vatican's position on the Holocaust amid the firestorm of controversy that broke out after Williamson's rehabilitation by the German-born pope.
Benedict last week expressed "full and indisputable solidarity" with Jews and warned against any denial of the horror of the Holocaust, but several leading German bishops have decried the German-born pope's decision and called for Williamson's rehabilitation to be revoked.
"I do not believe that sufficient clarification has been made," Merkel said.
The Vatican moved quickly to counter Merkel's suggestion.
"The pope's thinking on the subject of the Holocaust has been expressed very clearly," said Vatican spokesman Rev. Federico Lombardi.
He cited Benedict's visit to a synagogue during his first visit to Germany as pope in 2005, a visit to Auschwitz in 2006 and his remarks during last week's general audience.
Lombardi quoted from what he called the pope's "unequivocal words" at that public audience. "I hope that the memory of the Shoah leads humanity to reflect on the unpredictable power of evil when it conquers the heart of men," he quoted the pope as saying. "May the Shoah be a warning for all against oblivion, against denial or reductionism."
Lombardi said that during the audience "the pope himself clearly explained the purpose of lifting the excommunication, which has nothing to do with any legitimization of positions denying the Holocaust, which were clearly condemned" by Benedict.
The issue is particularly sensitive in Germany, where denial of the Holocaust is a crime and Roman Catholic leaders have worked hard to restore relations with the Jewish community.
As a young man in Germany, Benedict, then called Joseph Ratzinger, served briefly in the Hitler Youth corps.
Earlier Tuesday, Cardinal Karl Lehmann, the bishop of Mainz, called for an apology from "a high level."
"There must also be consequences for those who are responsible for this," Lehmann said in an interview with broadcaster Suedwestfunk of the decision to rehabilitate Williamson.
Williamson, in an interview broadcast last month on Swedish state TV (left), said that historical evidence "is hugely against 6 million Jews having been deliberately gassed in gas chambers as a deliberate policy of Adolf Hitler."
He cited what he called the estimates of the "most serious" revisionists that "between 200,000 and 300,000 perished in Nazi concentration camps, but not one of them by gassing in a gas chamber."
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