Anti-Catholic hostility is "deep and wide" in Scotland, a spokesman for the Catholic Church said today.
The comments follow reports SFA referees chief Hugh Dallas has left his post after claims he forwarded an offensive email about the Pope's recent visit to Scotland.
Earlier this week, Catholic Church spokesman Peter Kearney demanded Mr Dallas's dismissal if the allegations were found to be true.
In a newspaper article published today, Mr Kearney said that "tasteless" emails may simply be "the tip of a disturbing iceberg of anti-Catholicism in Scottish society".
He said: "Many people have claimed that emails similar to the one in question circulated widely in the weeks leading up to the Pope's visit. These comments are, incredibly, intended to somehow mitigate the culpability of those who were recently being accused.
"Sadly, they do nothing of the sort. Instead they illuminate the reality of a layer of deep, wide and vicious anti-Catholic hostility in our country."
Mr Kearney said such hostility has often been tolerated by Catholics, but that the recent episode has caused Scots Catholics to "draw a line in the sand".
He wrote: "I detect a new resolve, especially among younger people. Our grandparents and even our parents suffered intolerance and persecution. We will not tolerate it.
"We will not laugh it off or see the funny side - because there is no funny side. Beneath the surface of the nasty emails and the intemperate asides of public figures there are others whose malignancy is altogether more pernicious."
He said that recent examples of the intimidation of priests is only a snapshot of the intolerance suffered by Catholics.
"The bigotry, the bile, the sectarian undercurrents and innuendos must end," he said.
"Such hateful attitudes have had their day, they poison the well of community life, they must be excised and cast out once and for all."
Questions arose about Mr Dallas's future as the SFA's head of referee development after reports claimed a photograph relating to the Pope's September visit had been passed on via official SFA emails.
The photograph showed a road sign featuring a woman and a child with a doctored message referring to the Pontiff below.
Mr Kearney last week demanded swift action over the allegations, saying the email was "gratuitously insulting to the Pope, deeply offensive to the Catholic community of Scotland, and an incitement to anti-Catholic sectarianism".