The judgement was issued in November and the attorney general is currently considering whether to appeal.
The Catholic Church was recognised as an 'interested party', which gives it the right to be heard in court, and is arguing that there are many reasons for the ruling to be challenged.
The Secretary of the Catholic Council for Social Affairs, Tim Bartlett, said that even though rape is "the most heinous of crimes, the answer is not to take the life of an innocent third party. The challenge is to give that person every possible support and care."
The church also disagrees with the judge's claim that there is no life to be protected in cases of so-called fatal foetal abnormality.
"In the church, we work with women whose babies have life-limiting conditions, and these children can live for minutes, hours, days, weeks and in some cases years. The child is still technically, clinically and in every sense alive as a human person, and is entitled to have their life protected."
The largest Protestant denomination in Northern Ireland - The Presbyterian church - agrees with the Catholic church on this point, and is also opposed to the current law being eased.
However, Norman Hamilton, a former moderator of the Presbyterian church, said: "We have always taken the view, contrary to the Catholic church, that where the mother's life is in serious danger, or if there is substantial risk to mental health, then the law allows for abortion, and we are content with that."
Public opinion in Northern Ireland is widely seen to be shifting, leading to renewed debates on major social issues.
Gladys Ganiel, a research fellow at Queen's University Belfast, said: "Until a generation ago, the conservatism of the churches was reflected in public attitudes, but that has changed in the past 10-20 years.
"There's now a silent majority which is more liberal on issues such as abortion and homosexuality than their public representatives in politics or in the churches."