Cardinal Walter Kasper, in charge of relations with Jews, said the prayer used by an "extremely small" number of traditionalists on Good Friday simply expressed the Catholic view that Christ is the savior of all humankind.
It was not a step backwards in the Church's respect for Jews, he said, although he acknowledged the controversy was a sign of how difficult the interfaith dialogue can sometimes be.
"The reactions from Jews are in large part not motivated in a rational way, but in an emotional way. But one should not write them off too quickly as being caused by hypersensitivity," Kasper wrote in Vatican newspaper L'Osservatore Romano.
In February the Vatican revised a contested Latin prayer used by traditionalist Catholics on Good Friday, the day marking Jesus Christ's crucifixion, removing a reference to Jewish "blindness" over Christ and deleting a phrase asking God to "remove the veil from their heart".
Jews criticized the new version because it still says they should recognize Jesus Christ as the savior of all men. It asks that "all Israel may be saved" and Jews said it kept an underlying call to conversion that they had wanted removed.
Kasper said he realized that for many Jews, the collective memory of forced conversions in past centuries "is still alive".
"The new formulation of the prayer ... doesn't say anything truly new, but just expresses what until now was assumed to be obvious," Kasper wrote in the Italian-language article.
The reference to saving Israel was "eschatological", a reference to a branch of theology dealing with the destiny of all humanity at the end of the world.
Kasper said the Catholic Church, unlike some evangelical Churches, did not have an institutionalized directive to convert Jews although Catholics are always encouraged to express their faith openly while showing respect.
Last week, the Vatican issued a statement on the prayer saying it "in no way intends to indicate a change in the Catholic Church's regard for the Jews".
The Vatican said the Church's relations with Jews were still based on the 1965 Second Vatican Council statement Nostra Aetate, which repudiated the concept of collective Jewish guilt for Christ's death and began dialogue.
"One must always be mindful that dialogue between Jews and Christians will remain, by its nature, always difficult and fragile and that it demands a great amount of sensitivity from both sides," Kasper wrote.
Next week in the United States, Pope Benedict will meet American Jewish leaders and make a brief visit to the Park East Synagogue in Manhattan.
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