The Pope has rejected an invitation to address the European Parliament, amid Vatican alarm at what is seen as a drift towards militant secularism.

A letter from the Vatican said that he was declining the request to speak to MEPs owing to other commitments and his age, The Times has learnt. The rejection came soon after the Pope agreed to spend his 81st birthday visiting President Bush and as his tour of Australia was ending. The Parliament, which wanted the Pope to be principal Christian guest in its Year of Intercultural Dialogue, may resort to a less well-known Eastern Orthodox leader.

The Vatican has favoured the White House as a reward for Mr Bush’s acclamation of faith in God and help for antiabortion causes.

At a Mass held at a racecourse in Sydney yesterday the Pope, who has been celebrating Catholic World Youth Day, told 400,000 worshippers that in many societies, “side by side with material prosperity, a spiritual desert is spreading: an interior emptiness, a quiet sense of despair”.

Early today he met Australians who had been sexually abused by paedophile priests, after apologising at a Mass on Saturday for their suffering.

The breakdown in confidence between the Pope and the European Parliament is a sensitive area and observers close to the dispute are unwilling to be identified publicly. One spoke of the church hierarchy’s “great disillusionment” with the European project. Its founding fathers, Konrad Adenauer and Robert Schuman, were deeply Catholic. However, a well-informed observer said that the EU “has become more and more secularist”.

John Paul II addressed the Strasbourg Parliament in 1988. Since then there have been several clashes between the Vatican and the EU, culminating in dismay over the removal of “God” from drafts of the EU constitution.

The Pope’s refusal is particularly hurtful as the Parliament’s president is Hans-Gert Pöttering, a German Catholic and Christian Democrat. After he was elected president last year, Mr Pöttering visited the Vatican to celebrate the 50th anniversary of the Treaty of Rome. “He had a private audience and gave an invitation to the Pope to address the Parliament,” a spokesman for the presidency said.

The Vatican initially acknowledged that the request was being looked at, but early this year its Secretary of State said that the Pope would be unable to come “at least for 2008”.

The European Parliament has been trying to get leaders of world faiths to join its intercultural year. The Grand Mufti of Syria has already attended, Britain’s Chief Rabbi will do so and the Dalai Lama has an open invitation.

“Clearly the Pope is over 80 so they have to be very careful about not exhausting him,” the presidency spokesman said. Yet the Pope has made arduous trips to America and Australia. Mr Bush is regarded by the Vatican as far more sympathetic to its priorities than Europe. When he withdrew $34 million from the UN family planning programme in 2002, claiming that some money went to abortions, the European Union made up the shortfall.