The destiny of Europe is preoccupying the Vatican.
A Spanish newspaper accused the Pope of stirring "absurd tensions"
It has complained of a "militant secularism" which, it says, is driving the Church out of public life in Europe.
Cardinals have even complained of an "anti-Catholic inquisition".
They have pointed to policies such as France's ban on conspicuous religious symbols in schools, the EU's rejection of a reference to God in the proposed EU constitution and Spain's proposals to legalise gay marriage.
"In 2,000 years of the Church's existence, those trends have come and gone," Cardinal Martino, head of the Pontifical Council for Justice and Peace, told the BBC World Service's Assignment programme.
"There is a trend to exclude the Catholics, who are sent into a ghetto."
In England and Wales, the Catholic Church issued a pamphlet ahead of European elections, saying that voters should draw on religious teaching when they come to vote.
"There are matters that are common to both politicians and believers," Cardinal Martino said. "The Church has to have its say."
Some in the Vatican saw the case Rocco Buttiglione - a close personal friend of the Pope - as one of the most high-profile examples of secular views triumphing over Christian concerns.
Italy nominated Mr Buttiglione as EU Commissioner for Justice and Home Affairs, but he was rejected by MEPs after describing homosexuality as a "sin".
He told Assignment he felt he had been excluded "because of [my] religious beliefs."
"In a liberal state, you evaluate the political line and the political ideas of a candidate, and you do not impose upon him an inquisition, or a conscience police," he said.
"That is what has been done in the European Parliament against me."
Mr Buttiglione described the MEPs' stance as a "violation" of "the traditional liberal distinction between the public and private sphere".
This is not the first time the Vatican has complained about the impact of secularism.
After it lost the Papal States in 1870, the city state developed a distrust of secular rulers - with Pope Pius X complaining that "God has been driven out of public life by the separation of Church and state".
Some cardinals fear Catholics may be "ghettoised"
But Franco Pavoncello, a political scientist at John Cabot University in Rome, says he is "surprised" by Vatican fears that secular Europe and the Catholic Church may be on a collision course.
"If there is one overwhelming aspect of Europe, it is the homogeneity of religion," he said.
"This is a continent that has been characterised by its Christianity."
But Mr Pavoncello said it was possible there had been a "return to more militant Christian values" amongst some Europeans because of the influence of Islam.
The Pope has urged bishops in Spain to defend traditional values, in opposition to the ruling Socialist Party's reforms.
These reforms include allowing gay marriages - supported, polls suggest, by the majority of the population - and broad-based teaching of religion in schools, not just focusing on Christianity.
'Adapt without disappearing'
The Vatican says the reform programme is "promoting contempt or ignorance of religion".
But Spanish Justice Minister Juan Fernando Lopez Aguilar insisted that "we are just doing our job".
"We are accountable to the citizens, not to the Catholic Church.
"This is a secular society. We are ready to pay respect to every religious freedom in Spain, but we're also ready to promote our legislative initiative, and fulfil our duties."
Mr Aguilar stressed that the Catholic Church had "gone public, and very strongly so," with remarks that it is a "sin" to wear a condom, or to have sex before marriage.
"With considerations such as those... it is difficult to open room for compromise," he argued.
Father Vivas Sotto, of Spain's Family Forum group, said the government's proposals "don't just affect the Church - they affect all of society".
"When life's dignity is forgotten and abortion is promoted, when embryos are not considered, when the richness of marriage is undervalued, that fundamental part of society is being undermined," he added.
In the Spanish media, reaction to the Vatican's pronouncements has been mixed.
The daily El Pais accused the Pope of stoking "absurd tensions". But El Mundo urged both sides to "cool it".
"The message [from the government] is the Catholic Church is old, it's completely retrograde, it's associated with Franco and Francoism - that dark, inquisitorial Spain," said Kayatana Elvorez Detoledo, El Mundo's leader writer.
"That's not strictly true, of course. The Vatican has a very difficult problem to solve - how to modernise, but not to lose a fundamental moral principle. It has to adapt without disappearing."