Rt Rev Leo Cushely wrote to Tina Beattie, banning her from a talk at a Catholic group in Edinburgh because she disagreed with the Church's teaching on sexual morality.
Ms Beattie is the professor of Catholic Studies at Roehampton University in London and has previously been stopped from speaking at events in San Diego, California, and in Bristol.
It is thought that the Congregation for the Doctrine of the Faith (CDF) could have forced the archbishop to intervene and cancel the event.
Archbishop Leo wrote to the Newman Society advising them to cancel the event she was due to speak at, saying she was "known frequently to have called into question the Church's teaching".
He has not responded to requests for a comment.
Tina Beattie signed an open letter in favour of same-sex marriage while the bill was going through parliament.