Scotland's eight Catholic bishops said gender is "an unchanging principle of human existence" and not something that can be altered.
They have written to First Minister Nicola Sturgeon about the issue, as the government’s second consultation on proposed changes to the Gender Recognition Act closed yesterday.
They claim the changes the Scottish Government is proposing could be "damaging to those involved".
In their letter, the bishops stated: "The proposed changes risk creating medical, social and legal complications which will be difficult to resolve and damaging to those involved, particularly children and women.”
The reforms to gender recognition legislation would change the way transgender people are able to change their birth certificate. The proposals include removing the need for a medical diagnosis of dysphoria, reducing the length of time a person has to live in their adopted gender from two years to six months, and reducing the age which a Gender Recognition Certificate can be applied for to 16.
Trans rights campaigners have said the current process is "demeaning, lengthy, stressful and expensive", and instead want transgender people to be able to “self-declare” to gain a certificate.
The move has prompted the establishment of new women’s groups to campaign against the reforms, claiming they would impact on women’s rights to single-sex spaces, and allow predatory men easier access to vulnerable women.
However, other organisations such as Scottish Women’s Aid, Rape Crisis Scotland, and Engender, have said the reforms will have no impact on women.
The Catholic Church has now argued moving to self-declaration could mean some vulnerable people miss out on necessary support. "De-medicalisation removes a vital protection and safeguard for vulnerable individuals," they stated.
The bishops argued: "Together with a growing number of voices in society, the Church believes that sex or gender cannot be reduced to a mere construct of society that is fluid and changeable.
"Denying the biological reality of sexual difference and redefining something as fundamental as male and female is not within the purview of government or parliamentarians.
"Like marriage, it is part of the natural law - an unchanging principle of human existence."
They added: "Sex is constituted by biological organisation and reproductive functioning, and is recognised at birth, not assigned. Government should not proceed with radical legal reforms or expose children to radical treatments. Caution and sensitivity is required."
A Scottish Government spokesman said: "As with all consultations, all responses will be analysed and considered along with any other available evidence.
"An analysis report will be published when that work is complete."