Pope John Paul II has warned the new Archbishop of Canterbury, the head of the worldwide Anglican Communion, that "new and serious difficulties have arisen" in relations between the two Churches.
The head of the Catholic and Anglican church first met face-to-face in 1960
In what correspondents say was an indirect reference to homosexual clergy, the Pope told Archbishop Rowan Williams that Christians had to be protected from he called erroneous and misguided interpretations of the faith.
"These difficulties are not all of a merely disciplinary nature; some extend to essential matters of faith and morals," Pope John Paul II said.
There was however some progress on another stumbling block in Catholic-Anglican relations - in a prepared statement Dr Williams said he would respond to the Pope's invitation for suggestions about the future of Papal primacy.
The 15-minute private audience was the first time the two men had met.
The Pope suffers from Parkinson's Disease and arthritis
They exchanged gifts and in an effort to show that relations between their churches were improving Dr Williams wore the Episcopal ring given to one of his predecessors by the late Pope Paul VI, and a gold cross which the present Pope sent him on his enthronement earlier this year.
There has been much speculation in recent weeks about the 83-year-old Pope's state of health.
But the BBC's David Willey, in Rome, says he seemed alert and - although hampered in his speech by the Parkinson's Disease that afflicts him - fully engaged in the conversation.
Fears about the pontiff's health were heightened when Austrian Cardinal Christoph Schoenborn said he might only have a short time to live.
Cardinal Cormac Murphy O'Connor, the Archbishop of Westminster, who was also present for the meeting rejected claims that the Pope's demise was imminent.
"I think it's quite clear that the Pope is frail. But every day he's there, every day everyone can see him... His mind is very clear and therefore I would have thought no need for immediate alarm at all," he said.
The ordination of homosexual priests has split member of the Anglican Church between supporters and opponents of the controversial issue.
On Friday, Cardinal Walter Kasper told Vatican radio he had expressed "concern" to Dr Williams on the issue of homosexual priests.
He said it was "not only an internal problem of the Anglican Communion, but it also impinges on our ties".
Analysts say the words are likely to add to Dr Williams' difficulties on the issue.
The heads of the Catholic and Anglican Churches first met face-to-face in 1960, and this has since become a regular event.
A spokesman for Lambeth Palace said: "The fact that there are now routine visits is something that would not have been the case even 20 or 30 years ago.
"It is a very recent thawing of relations between the two Churches."