The source of the dispute, which Austrian media has dubbed Vienna's version of the Mohammad caricature row, is a retrospective honouring Austria's cherished artist Alfred Hrdlicka. He turned 80 earlier this year.
But not everyone has been wishing Hrdlicka a happy birthday. And the cathedral's museum director and Cardinal Christoph Schoenborn - the Archbishop of Vienna - have both come under fire from some museum visitors and Catholic websites.
The church hastily removed the main picture - "a homosexual orgy" of the Apostles as Hrdlicka describes it.
But the protest has continued, much to the surprise of the cathedral.
The cathedral's museum director has defends both Hrdlicka's work and his decision to host the artist's controversial versions of biblical imagery in a museum tied to the Catholic Church.
"We think Hrdlicka is entitled to represent people in this carnal, drastic way," Bernhard Boehler said in his small office, across the street from Vienna's imposing St Stephan's Cathedral.
He says the museum never intended to offend people, but that art should be allowed to provoke a debate.
"I don't see any blasphemy here," he said, gesturing at a crucifixion picture showing a soldier simultaneously beating Jesus and holding his genitals. "People can imagine what they want to."
Mr Boehler says that picture drew particular criticism from some visitors, along with a sculpture of Jesus on the cross without a face or loincloth.
But the most disputed work was Leonardo's Last Supper Restored By Pier Paolo Pasolini, which showed cavorting Apostles sprawling over the dining table and masturbating each other.
Hrdlicka says he represented the men in this way because there are no women in the Da Vinci painting which inspired it.
Pasolini was a controversial Italian film-maker and writer who was murdered in the 1970s.
Fierce criticism
The exhibition has attracted fierce criticism on religion blogs in Austria, Germany and even in the United States, with bloggers denouncing it with terms such as "blasphemy" and "desecration".
"The exhibition should never have taken place. The director should apologise to Catholics worldwide for this," an article on conservative Catholic website kreuz.net said.
In the United States, conservative columnist Rod Dreher wrote on his widely read blog: "I wouldn't have guessed that, given his reputation, a man like [Cardinal] Schoenborn would have stood for this abomination for half a second."
The museum took down the piece at Cardinal Schoenborn's request just over a week after the Religion, Flesh And Power exhibition opened, leaving a blank black wall at the entrance to the display.
"This has nothing to do with censorship, rather corresponds with the understood 'reverence for the sacred'," the Cardinal's spokesman said in a statement.
"It is also an act of respect towards those believers who feel this portrayal offended and provoked them in their deepest religious sensitivity."
Artist's response
The diocese says the museum's decision to show Hrdlicka's work does not mean it identifies with everything it portrays.
Hrdlicka agrees, but points out that the piece was not intended as a swipe at the Catholic Church.
"There was such a reaction to its physicality. For me it was quite surprising the museum wanted to show the piece in the first place," he told Reuters by telephone. "If the museum is having problems now, it's not really my affair. It's for the museum to deal with."
Hrdlicka says overall he is pleased with the display and has praised the director for being "strong".
A communist and atheist, Hrdlicka once said the Bible was the most thrilling book he had ever read and that religious imagery forms a central core to his work.
Missing the point
Mr Boehler says the angry emails he has received remind him of how some reacted to Mel Gibson's 2004 film The Passion of The Christ. In his opinion, critics of the film's violence and physicality also missed the point.
"The crucifixion was brutal and it would be a lie to say everything in our world is nice," he said, pointing out that Hrdlicka is an anti-war activist who has seen the effects of Nazism and violence first-hand.
"We in Europe have been affected by this and it influences how we see [Hrdlicka's] work."
Mr Boehler, like Hrdlicka, says the art debate can be compared to the Danish cartoon row - where an image of the Prophet Mohammad with a bomb in his turban enraged some in the Muslim world who saw it as blasphemous.
The angry reaction to Hrdlicka's work has only been verbal and the museum acknowledges some Christians have been balanced and support the exhibition, despite disagreeing with the artist's approach.
Curator Martina Judt says the exhibition was meant to prompt this kind of balanced reaction.
"People have said the Catholic Church has become a lot more liberal," she said.
"But in the end, the reactions show this perhaps isn't the case."
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