Bishop Bernard Fellay, head of the rebel Society of Saint Pius X (SSPX), said last month that Jews were among those "who over centuries have been enemies of the Church".
Jewish support for the modernizing reforms of the 1962-1965 Second Vatican Council showed they were opposed to the Church, he said. The SSPX rejects the Council as a heretical event that betrayed age-old Catholic teaching and undermined the Church.
"It is impossible to speak of the Jews as enemies of the Church," Vatican spokesman Rev Federico Lombardi said, stressing the Church position on this was "clear and well-known".
"The Church is deeply committed to dialogue with Jews," he added.
Fellay was among four SSPX bishops who were excommunicated from 1988 to 2009, when Pope Benedict reinstated them.
Talks between the SSPX and the Vatican to reintegrate them fully into Church structures ended in failure last year because the SSPX refused to accept Council reforms - including Rome's reconciliation with the Jews - as valid Catholic teaching.
The Simon Wiesenthal Center in Los Angeles, a Jewish human rights group, denounced Fellay's comments last week as a sign of "the deep-rooted anti-Semitism that lies at the heart of the SSPX's theology".
The Second Vatican Council "shifted the relationship between Catholics and Jews into a positive direction", it said.
One of the four excommunicated SSPX bishops was Richard Williamson, who deeply embarrassed the Vatican by denying the Holocaust on Swedish television only days before he and the others were reinstated by the Vatican.
He has since been expelled from the group and is fighting charges of Holocaust denial in a German court, which took up the case because the television interview was filmed in Germany.
(Reporting by Tom Heneghan; Editing by Alison Williams)