The Church said there needed to be "room for debate and a robust exchange of views" as it warned that holding to Catholic beliefs, particularly on marriage or sexuality, may soon be deemed "an attempt to stir up hatred".
The warning was made in a submission to the Scottish Government's consultation on hate crimes following a review last year by Lord Bracadale.
The consultation, which closed last month, asked members of the public for their responses to Lord Bracadale's report on hate crimes in Scotland in which he recommended that a protection of freedom of expression provision be included in any new legislation relating to stirring up offences.
The Church welcomed the proposed protection for freedom of expression but said it was concerned that the definition of hate was becoming "contentious and open to misuse".
"Care must be taken to allow room for debate and a robust exchange of views, ensuring that 'hate' doesn't include the kind of ordinary discourse where people reasonably hold divergent views," the submission states.
"The fundamental right to freedom of expression, and the right of an individual to hold and express opinions, even if they are considered by some to be controversial or unwelcome must be upheld."
The Church further warned that changes to hate crime laws may hinder, rather than help, community relations. This was a particular risk, it said, in communities where sectarianism is an issue.
Catholic Parliamentary Office Director Anthony Horan said: "We do not believe there is a need for sectarianism to be specifically addressed and defined in hate crime legislation. Existing legislation, including existing statutory aggravations, are adequate."
He went on to warn that suppressing the right to freedom of expression would "create divisions and foster grievances across society".
"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," he said.
"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 definition of hate crimes in Scotland was called into question last year when the Scottish Police launched a series of controversial billboard posters aimed at tackling hate crime.
The posters were criticised by Christians who felt that they unfairly implied that they were bigots.
One particularly contentious poster read: "Dear Bigots, you can't spread your religious hatred here. End of sermon. Yours, Scotland."
The posters were withdrawn following a formal complaint by Barnabas Fund, a charity that supports persecuted Christians around the world.
According to the charity, Police Scotland "investigated themselves and belatedly responded in December, concluding that there was no case to answer and no further action would be taken".