Prof John Haldane, who is a professor of philosophy at St Andrews University and papal adviser to the Vatican, told a special Newsnight Scotland debating panel that the church only learned of the allegations nine days ago.
Catherine Deveney wrote The Observer piece in which three serving priests and one former priest accused the cardinal, who has now stepped down from public office, of "inappropriate behaviour" towards them.
She told the debate: "It is not quite accurate to say the Scottish Catholic Church did not know what was going on because there was an intermediary within the Catholic Church who took the complaints to the Papal Nuncio."
Prof Haldane said he was aware of the intermediary who had brought the accusations straight to Rome as opposed to beginning a complaints procedure within the Scottish Catholic Church.
However, he insisted that the first the church in Scotland knew the details of the claims was the night prior to publication of The Observer story.