Responding to a government consultation on Scotland's hate crime laws, leaders said Scotland risks becoming an "intolerant, illiberal society" unless there is space for "robust debate and exchange of views".
Catholic Parliamentary Office Director, Anthony Horan said: "In a climate of heightened sensitivity, there is a very real danger that expressing or even holding individual or collective opinions or beliefs will become a hate crime. We must guard against this and ensure freedom of expression, thought, conscience and religion are protected.
"Some people might suggest that expressing the Catholic Church's position on marriage or human sexuality could be an attempt to stir up hatred. This would obviously be wrong, but without room for robust debate and exchange of views we risk becoming an intolerant, illiberal society."
The Catholic Church in Scotland also warned of a "growing hierarchy" of protected characteristics listed in hate crime legislation, as they argued against the introduction of a new sectarianism category.
The Scottish Government consultation on hate crime follows a review by Lord Bracadale which recommended fresh protection for free speech to be included in any new hate crime legislation.
Mr Horan added: "Existing legislation, including existing statutory aggravations, are adequate.
"We would oppose any move to shift existing protections to an unnecessary sectarianism aggravation and agree with Lord Bracadale that the absence of such an aggravation would not leave a gap in the law as both race and religion statutory aggravations can be attached to any base offence if proven."
"Christian communities in Scotland enjoy a positive ecumenical relationship and we are concerned that government is proposing unnecessary legislation that undermines the development of community relations between them.
"The proposed aggravation assumes, wrongly, that where anti-Catholic, anti-Protestant, anti-Irish or anti-British bigotry or racism occurs, those responsible are from another Christian denominations or Irish/British ethnicity."
Last month, a Scottish minister apologised for any offence caused after a poster campaign aimed at those engaging in hate crime left some people of faith feeling targeted.
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