Cardinal Thomas Collins wrote to the Liberal leader Wednesday to say he is deeply concerned about the controversy.
Collins said he understands the need for party discipline, but questions whether that discipline can extend to matters of conscience.
"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," Collins wrote.
"But that political authority is not limitless: it does not extend to matters of conscience and religious faith. It does not govern all aspects of life."
Trudeau has said the party won't accept new candidates who are not pro-choice on abortion, although sitting MPs will be allowed to run even if they oppose the practice.
"As a party, we are steadfast in our belief ... that it is not for any government to legislate what a woman chooses to do with her body, and that is the bottom line there," Trudeau said last week.
"I have made it clear that future candidates need to be completely understanding that they will be expected to vote pro-choice on any bills."
In his letter, the cardinal reminded Trudeau — who was raised in the Catholic faith of his famous father — that the patron saint of politicians, Thomas More, was executed for following his conscience against the political authority of his day.
Collins pointedly mentioned that there are two million Catholics in his diocese. He said he encourages them to get involved in politics as both voters and candidates.
"It is not right that they be excluded by any party for being faithful to their conscience."
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