As the furor over the issue continues, the Liberal leader was asked at an event in Toronto whether he would sit down with Ottawa Archbishop Terrence Prendergast to discuss his views on abortion.
"I have a lot of respect for his eminence and for any leaders within the church, but I do want to highlight that he has a very different role than I do," said Trudeau, who was raised Roman Catholic.
"My role is to stand up and defend all Canadians and my role in terms of that is separate from any personal religious views."
The Liberal leader didn't elaborate on whether he would meet with Prendergast.
The Ottawa archdiocese said that Prendergast doesn't want "to judge his conscience," but a meeting "would be a good idea."
Bishop Christian Riesbeck said that if the Liberal leader refused a meeting and continued to practise his Catholic faith in the form of receiving communion, it would be unseemly.
"It's the fact that he considers himself to be a devout Catholic but then adheres to, or advocates for, abortion," said Riesbeck.
"That is scandalous," he said, as opposition to abortion has been a clear and unchanging teaching of the church.
Bishop calls for public retraction
Riesbeck is also not convinced by the argument that the Liberal Party is the party of the Charter of Rights and Freedoms and will support women's rights.
"You know, if you look at Article 7 in the charter, it says that everyone has a right to life. It's enshrined right there," said Riesbeck.
"Article 2 also speaks of freedom of conscience and religion. He seems to have undermined those values that all Canadians hold dear."
Riesbeck said that if Trudeau wanted to make things right, he would have to reverse course.
"Ultimately, he would have to make a public retraction of his views," he said.
The Catholic community has come out strongly against Trudeau over the past couple of weeks, with leaders from various dioceses criticizing the Liberal leader for what they say is a move that excludes people from political participation.
"Political leaders surely have the right to insist on party unity and discipline in political matters which are within the legitimate scope of their authority. But that political authority is not limitless: it does not extend to matters of conscience and religious faith," wrote Toronto Archbishop Thomas Collins in a May 14 letter to Trudeau, urging him to reverse his pro-choice rule.
Trudeau 'more extreme' than PM Harper
Rev. Raymond de Souza, a Roman Catholic priest, also recently penned a sharp column in the Catholic Register.
"I have criticized Prime Minister Stephen Harper for his refusal, as he puts it, 'to reopen the abortion debate.' Justin’s position is even more extreme than that," wrote De Souza.
"It proposes getting rid of the abortion debate altogether by inviting one side to surrender to the other. Pro-life Canadians will decline the invitation."
It's not the first time a Liberal leader has fallen out of favour with the Catholic Church.
When Prime Minister Paul Martin introduced legislation legalizing same-sex marriage in 2005, Pope Benedict condemned political double standards when it comes to religion.
"The type of tolerance which permits God as a private opinion but refuses to allow him in the public arena, is, in the reality of the world and our life, not tolerance but hypocrisy," said the pope.
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