The "Berlin Declaration" was issued by German Chancellor Angela Merkel, current holder of the rotating EU presidency, to mark 50 years since the founding of the union in Rome in 1957.
The declaration highlights European values such as democracy and outlines a vision for the future which includes fighting climate change. It contains, however, no reference to God or to Europe's Christian roots.
In a hard-hitting speech to European bishops, the Pope accused Europe of abandoning God and the Christian faith - the dominant faith across the continent.
"If on the 50th anniversary of the Treaty of Rome the governments of the union want to get closer to their citizens, how can they exclude an element as essential to the identity of Europe as Christianity, in which the vast majority of its people continue to identify," he said in a Reuters report.
"Does not this unique form of apostasy of itself, even before God, lead it (Europe) to doubt its very identity?"
The Pope has, likewise, advocated strongly for a reference to God in the EU constitution, following in the footsteps of his predecessor John Paul.
Chancellor Merkel, the daughter of a Protestant pastor, attempted to revive the debate on a 'God clause' in the EU constitution last year after visiting the Pope at his summer residence near Rome.
She has dropped any reference to God or Christianity in the latest declaration, however, in an effort to ensure the support of secular nations, namely France, which has repeatedly blocked any reference to God in the EU constitution.
At a meeting attended by Merkel and other EU leaders, the European People's Party, meanwhile, went against the tide of secularism and included a reference to Europe's Christian roots in its anniversary declaration.
"Europe's Judeo-Christian roots and common cultural heritage, as well as the classic and humanist history of Europe and the achievements of the period of enlightenment, are the foundation of our political family," said the statement.
Pope Benedict warned that the EU was on a slippery slope towards indifference, adding that it could not deny its "historical, cultural and moral identity" forged in large part by Christianity, reports Reuters.
"A community that builds itself without respecting the true dignity of the human being, forgetting that each person is created in the image of God, ends up doing good for no one," he said.