The controversial work was exhibited in Vienna's Cathedral Museum as part of a retrospective honoring Austria's renowned artist Alfred Hrdlicka, who recently turned 80.
Cardinal Christoph Schoenborn, archbishop of Vienna, said he had backed the exhibition without knowing the detailed contents.
"I obviously would not have agreed to have blasphemous or pornographic works exhibited. I therefore explicitly regret that a work of this kind was exhibited without my knowledge," the cardinal said in a statement.
The cardinal told the museum to take down the picture, "a homosexual orgy" of the Apostles as Hrdlicka describes it, just over a week after the display opened, after some visitors complained and it provoked a fierce uproar on Catholic websites.
Protest has continued over the picture 'Leonardo's Last Supper, restored by Pier Paolo Pasolini' which showed cavorting Apostles lounging on the dining table and masturbating each other. It was supposed to be a highlight of the display.
"In some of (the pictures) he oversteps the essential threshold of respect for the sacred," the cardinal said, adding that the museum does not identify with all of the works.
But he also defended Hrdlicka as one of Austria's most notable living artists who deserved such a retrospective.
"Hrdlicka...probably more than any other living artist, has devoted himself to the suffering and downtrodden human being and has appealed for "compassion" with the "Passion," he said.
The museum has said it did not set out to offend people but has defended Hrdlicka's work and the decision to display the controversial versions of biblical imagery.
Schoenborn, a former student of Pope Benedict who edited the Catholic Church's official catechism in the 1990s, maintains that art inspired by the Bible should be celebrated.
"I still hold the opinion that we must welcome the fact that artists who do not share our faith, or are still searching for belief, occupy themselves so intensively with biblical subjects," he said.
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