On Monday, the text, Male And Female He Created Them, was released 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.
Pope Francis has repeatedly argued the position that people cannot choose their genders.
In a statement in response a spokesperson for CBCEW said it was a welcome contribution to developing Catholic thought on gender, but reiterated the Church wanted to support those who are transgender.
"We recognise that there are people who do not accept their biological sex," it said. "We are concerned about and committed to their pastoral care.
"Through listening to them we seek to understand their experience more deeply and want to accompany them with compassion, emphasising that they are loved by God and valued in their inherent God-given dignity.
"There is a place of welcome for everyone in the Catholic Church."
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