Speaking at the Humbert Summer School in Co Mayo on Sunday, Cardinal Sean Brady was quoted by the Irish Times as saying that Ireland's rejection of the EU reform treaty in June suggested that "at least some of those who were previously enthusiastic about the founding aims of the EU, both social and economic, are now expressing unease".
There was, he continued, "a fairly widespread culture in European affairs which relegates manifestations of one's own religious convictions to the private and subjective sphere".
He pointed to what the late Pope John Paul II termed a "loss of Christian memory" within European institutions and policy-making bodies.
The "prevailing culture and social agenda" within the EU appeared to be dominated by secularism "rather than by the Christian memory and heritage of the vast majority of member states", said Cardinal Brady.
The Cardinal was invited to deliver the Bishop Stock address at St Patrick's Church of Ireland Cathedral in Killala as part of the Humbert school, which drew to a close on Sunday.
He told the audience: "Successive decisions... have undermined the family based on marriage, the right to life from the moment of conception to natural death, the sacredness of the Sabbath, the right of Christian institutions to maintain and promote their ethos, including schools.
"These and other decisions have made it more difficult for committed Christians to maintain their instinctive commitment to the European project.
"Ignoring this trend within the EU and its impact on people of faith has inevitable political and social consequences, not least on levels of support for the project itself."