Church spokesman Peter Kearney has said that Scotland is a hostile place for Catholics.
Kearney revealed he received 1000 emails from followers of Richard Dawkins attacking him after the atheist posted on his blog that Mr Kearney was "a nasty little weasel" for urging the SFA to fire its head of referee development, Hugh Dallas, for forwarding an offensive email cartoon of Pope Benedict before his visit to Scotland.
"Scotland remains a hostile environment for Catholics to live in. Priests have bricks thrown through their bedroom windows," said Kearney, according to HearldScotland.com
"The number of crimes motivated by anti-Catholic intolerance has gone up every year since the 2003 Criminal Justice Act was created. Things are not getting better."
Kearney also talked about how he dealt with the controversy surrounding former boss Cardinal Keith, who admitted inappropriate sexual conduct before going into exile.
He said: "I'd never handled anything like that before. The sheer scale of it was bigger than anything I'd ever dealt with, including the Pope's visit to Scotland in 2010.
"I'd already made arrangements for broadcast journalists to interview Cardinal O'Brien in Rome after the conclave, so it was easy for them to switch swiftly to this new development.
"I got 100 calls that Saturday night alone. They all wanted to know: 'Is it true about the allegations of inappropriate sexual behaviour? Is he going to the conclave?'"
He said he knew nothing of Cardinal Keith's misconduct.
"It was really, really difficult to find myself in the position of asking those sorts of questions to someone I'd worked with very closely over the years."
The crisis made him stronger. "My voice is heard, my advice is taken, and there is respect given [from Church colleagues]."