By Jane Little
BBC religious affairs correspondent
The Vatican has been drawn into a row over the nomination of Italy's Rocco Buttiglione as EU justice and home affairs commissioner.
The Pope has said moral relativism is threatening society
The conservative Roman Catholic is said to be a friend of Pope John Paul II.
His rejection by a European Parliament committee amounts to anti-Catholic bias, according to senior cardinals.
Moves to legalise gay marriage in Spain and ban religious symbols in French schools have also fuelled the sense of anti-Catholic discrimination in Europe.
It looks like the Vatican is fighting a rearguard action to maintain its political influence in Europe.
Sergio Romano, a political commentator on the Italian newspaper Corriere della Sera, says it is losing the battle.
"They feel they are defending themselves, they live in a state of siege. This is a sort of tragic end of papacy in a sense," he said.
"The Pope has conquered the world in his own image but he is losing the battle in Europe."
The Vatican failed, despite much effort, to get a reference to Christianity included in the EU constitution and the case of Mr Buttiglione has caused cracks to appear in the usual diplomatic front.
Cardinal Renato Martino, head of the Vatican's Council for Justice and Peace, says there is an anti-Catholic "Inquisition" in Europe.
Buttiglione expressed regret over his comments about gays
It may seem curious that he chose to draw a parallel with the Church's darkest chapter, when it burnt heretics at the stake - but that is a reflection of the depth of feeling at the Vatican.
The Pope often blasts moral relativism and recently said that it was threatening democracy.
But to many it is the Church's recourse to "Absolute Truth" that is the real threat. There is a heated debate going on among Catholics about the role of the Church within a democracy.
One commentator lamented that the Church expected Catholics to behave as obedient children of the Pope, when as citizens of Europe they must be sceptical and questioning as they work for the common good.
We cannot be expected to switch between the two, he said.