Pope John Paul II told the archbishop of Canterbury on Saturday that the acceptance of openly gay clergy members by many Anglicans presented "new and serious difficulties" in relations between the two churches.
His remark came during the first meeting here between the pope and the current archbishop, Rowan Williams, the spiritual leader of more than 75 million Anglicans worldwide.
Archbishop Williams assumed that post earlier this year and soon confronted a furious debate over homosexuality that threatens to rend the Anglican Communion. Its American branch, the Episcopal Church USA, recently appointed an openly gay bishop for New Hampshire.
The pope did not explicitly mention that on Saturday. But he was obviously referring to the issue when he assessed the state of relations between Anglicans and Roman Catholics.
"As we give thanks for the progress that has already been made, we must also recognize that new and serious difficulties have arisen on the path to unity," John Paul said, reading from prepared remarks in the papal library.
"These difficulties are not all of a merely disciplinary nature," he added. "Some extend to essential matters of faith and morals."
At a subsequent news conference, Cardinal Walter Kasper, head of the Vatican office in charge of relations with other Christian denominations, made clear that one of those matters was homosexuality.
Archbishop Williams, seated beside him, said the Vatican's concern weighed very heavily on him as he looked toward an emergency meeting of the Anglican Communion's leaders in Britain later this month. Its focus is the issue of homosexuality.
"We have listened hard in these last days," Archbishop Williams said, referring to the conversations that he and his aides held with Vatican officials on Friday and Saturday.
The pope did not attend the news conference.
His earlier meeting with Archbishop Williams was extremely brief. They spent about 10 minutes in private together and then read prepared remarks, in English, to each other in public.
There were long pauses between many of the pope's words, some of which were barely discernible.
John Paul, 83, suffers from Parkinson's disease among other ailments, and over the last few weeks he has had more trouble expressing himself.
His struggle against severe physical limitations is now so visible that some church leaders have begun to talk candidly about the tenuousness of his health and possible nearness of his death.
Although his remarks today were not lengthy, they were emphatic.
"Faced with the increasing secularism of today's world," he told Archbishop Williams, "the church must ensure that the deposit of faith is proclaimed in its integrity and preserved from erroneous and misguided interpretations."
Homosexuality has proved to be a divisive issue for many religions and denominations.
As Vatican officials draw up new guidelines for admissions to Roman Catholic seminaries, they are contemplating whether to bar men with an apparently homosexual orientation, even if those men profess to be ready, like their heterosexual counterparts, to commit to celibacy.
The existence and acceptance of openly gay Anglican clergy members like the New Hampshire bishop, V. Gene Robinson, who has a longtime male partner, challenge Roman Catholic tradition and teaching.
In late July, the Vatican issued a document that opposed legal recognition for same-sex couples. "Homosexual acts go against the natural moral law," it said.
Over the last four decades, the Catholic Church and the Anglican Communion have enjoyed a generally warm rapport, although there were sharp tensions when Anglican churches began ordaining women.
At the news conference, both Archbishop Williams and Cardinal Kasper emphasized the warmth of that relationship.
"I hope that none of what we have achieved over these many years of friendship will be lost," the archbishop said.
But Cardinal Kasper also said that the way in which the Anglican Communion moved forward in dealing with gay clergy members "could cause new problems for our relations."
"I hope and pray," he said, "that the Anglican Communion will find a constructive solution to the present situation, both for the sake of the Anglican Communion itself and for the sake of our relations as well."