Kemi Badenoch took a swipe at LGBTQ+ charity Stonewall while unveiling the Government's new trans guidance for schools.
She said the Governemnt "fundamentally disagrees" with the group's analysis, claiming they are giving schools "very bad advice".
The Government unveiled its new guidance for schools this morning, which says they should "take a very cautious approach" if pupils want to change their names, pronouns or uniforms.
The guidance - applying only to schools in England - says teachers do not have a "general duty" to allow pupils to socially transition.
Kemi Badenoch took a swipe at LGBTQ+ charity Stonewall while unveiling the Government's new trans guidance for schools
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It urges them to exercise caution, including "watchful waiting periods, and ensuring parents are fully consulted before any decision is taken."
Speaking about the new guidance, Badenoch said: "What we are doing is making sure that for those schools that are very unsure about what to do and are getting very bad advice from organisations like Stonewall - among others - understand what the Government believes should be done.
"And this is based on legal certainty. This is based on what the law says.
"The guidance has five pirnciples and two of them are based around understanding the legalities around safeguarding, and understanding the realities around biological sex.
"There is no general duty to socially transition a child.
"A lot of schools think this is something they have to do, or should be doing - and we are making sure they understand what the law says."
Stonewall has said there is considerable evidence that social transition improves the mental health of trans-gender young people.
Asked about this, Badenoch said: "No that is not something I am concerned about, and I should stress that we fundamentally disagree with Stonewall's analysis.
"We fundamentally disagree with their facts."
A school leaders' union has warned that headteachers will continue to be placed in a difficult position, claiming the Government’s transgender guidance leaves many “questions unanswered”.
Paul Whiteman, general secretary of school leaders’ union NAHT, said: “The ongoing delays to this guidance due to political wrangling have been a source of significant frustration, and it is far from ideal for it to be published right at the end of term, after some schools have already broken up for Christmas.
“NAHT will be reviewing these draft proposals to ensure they provide useful information and support for school leaders and will submit a response to the Government’s consultation on behalf of our members.
“Upon an initial look, it would appear this guidance leaves a lot of questions unanswered, meaning school leaders will continue to be placed in an incredibly difficult position.”
Stonewall has been contacted for comment.