Speaking on his show today, Mr D'Arcy refused to retract the statement.
"When I was referring to the Catholic Church, and I thought people would take this to be the case, I was referring to the hierarchy of the Catholic Church, not to people like my mother who is a devout Catholic and a great Christian."
He added: "I never meant to cause offence to them. And it is the hierarchy of the Catholic Church who have taken offence and are demanding an apology. That won't be forthcoming. There won't be a retraction. Because in my opinion the institution of the Catholic Church has caused well documented damage to the country and you don't need me to go through the litany of the documented things they have perpetrated."
Church leaders are furious that the country's most popular DJ was allowed to air his controversial views on his Today FM show.
D'Arcy's production team were locked in talks on the matter right up to the start of his programme this morning.
The Communications Office of the Irish Bishops has demanded a full apology saying the comments were "insulting".
The former children's TV presenter told his 245,000 listeners on Friday that the Catholic Church had, in many ways, "f***ed up this country".
He was discussing the now infamous comments made by Fine Gael TD Michelle Mulherin who sparked outrage by claiming 'fornication' was the main cause of unwanted pregnancies.
A spokesperson for the Church revealed at the weekend that the matter would be referred to the BAI in the form of a formal complaint unless an apology is made.