The clergyman, who was the chaplain at the school in the 1970s, then started dating the girl's mother after he left the priesthood.
The scandal only emerged four decades later when the victim, who is now 58, went to police to report the abuse.
The Catholic Church has distanced itself from Flannery, denied that the celibacy rule was off-putting and said there were 12 priests ordained in Scotland last year, the highest number in 20 years.
Flannery was suspended by the church in 2012 and threatened with ex-communication unless he stayed silent, but he is set to bring his message to Scotland on February 28 and risk further sanctions by the church.
“The Australian investigation into child sexual abuse in institutions, in the final summing up which came out a month ago, suggests compulsory celibacy was a factor.