The document insisted that modern gender ideology and the idea that one chooses or discovers his or her gender go against nature by arguing that "the only thing that matters in personal relationships is the affection between the individuals involved, irrespective of sexual difference or procreation, which would be seen as irrelevant in the formation of families".
The statement also called the Vatican's document "a gross misrepresentation of the lives of LGBT people which perpetuates and encourages hatred, bigotry, and violence against them".
Francis DeBernardo, the ministry's executive director, said it would confuse those struggling with questions of gender identity and sexual orientation - and could lead to self-harm, addiction and even suicide.
The text, Male and Female He Created Them, was meant to help Catholic teachers, parents, students and clergy address what the Vatican's Congregation for Catholic Education called an "educational crisis" in the field of sex education.
It's a sign that the church is not changing, and it's most hard for LBGT Catholics who are still committed to their faith.
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"We should welcome the congregation's call to dialogue and listening on gender, and I hope that conversation will now begin".
It calls for dialogue but it notably criticises the modern understanding of gender saying it is "often founded on nothing more than a confused concept of freedom in the realm of feelings and wants". The Vatican is the headquarters and governing body of the Roman Catholic Church.
It denounced theories that attempted to "annihilate the concept of nature" and "educational programs and legislative trends that. make a radical break with the actual biological difference between male and female".
Though Pope Francis didn't sign the document, the Congregation for Catholic Education cited the pontiff in its justifications.
And while great care must be taken to respect and provide care for persons who "live situations of sexual indeterminacy", those who teach in the name of the Catholic Church must help young people understand that being created male and masculine or female and feminine is part of God's plan for them.
"We recognise that there are people who do not accept their biological sex", it said.
"The document is mainly a dialogue with philosophers and theologians, and with other church documents", he said in a tweet, "but not with scientists and biologists, not with psychologists, and certainly not with LGBT people, whose experiences are given little if any weight".