Cardinal Keith O'Brien said that headteachers must remain vigilant of health boards or local councils pushing an agenda which failed to take account of the Church's "own Christian understanding of the human person and of human sexuality".
Cardinal O'Brien also attacked critics who had called for a withdrawal of funding from Catholic schools if they did not deliver exactly the same services as every other school, following publication of the Scottish Executive's sexual health strategy.
Such comments, he told the annual Catholic Headteachers' Association of Scotland conference in Crieff yesterday (Thursday), showed ignorance of the recommendations of the McCabe report on sex education in schools and subsequent guidance.
These documents had made clear that the Church had the right to provide guidance to schools on the teaching of sex education and that the headteacher was responsible for determining the content and delivery of sex education in accordance with the values of the school community.
At the time of publishing its sexual health strategy, the Executive insisted that any head, in conjunction with a local authority, had to consult on how best to deliver sex and relationships education within the guidelines. There was sensitivity in that respect but not a "blanket opt-out".
An Executive spokesman stated: "The important thing is that Catholic schools will not be able to decide not to teach sex education or talk about contraception."
Cardinal O'Brien told headteachers yesterday that the Executive's guidance offered "important guarantees which ensure that you have control over the approaches taken in your school to deliver appropriate relationships and moral education for young people".
He urged heads to ensure staff were familiar with guidance from the Scottish Catholic Education Service on how to agree protocols with various agencies, ensuring they respect Catholic values.
He stated: "This is a very important issue which will affect the lives of our young people and the welfare of families. We need to show that the Catholic school is offering them an alternative vision to what is on offer elsewhere. We need to explain the Church's teaching positively and we need to provide full and accurate information with a view to developing fully informed consciences in our students."
The Cardinal, recently returned from the conclave in Rome that elected the new Pope, told heads he did not underestimate the challenges of their job.
"I am well aware that many of your students are not participating in the faith community that is their local parish. Some have not learnt at home even the basics of our faith."
Four questions for heads
* How "authentic" are you in terms of being a witness to your faith?
* How confident are you in your knowledge of the faith?
* How confident are you that your overall school community takes seriously its mission to be "at the heart of the Church"?
* How are the values of the Gospel understood, taught and lived in your school community?