In what was seen as an indirect reference to homosexual clergy, the BBC reported the Pope told Archbishop Rowan Williams that Christians had to be protected from what 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," the Pope was quoted as saying.
The 15-minute private audience was the first time the two men had met.
There was some progress on another stumbling block in Catholic-Anglican relations, BBC said.
In a prepared statement, Williams said he would respond to the Pope's invitation for suggestions about the future of Papal primacy.
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