Ms Badenoch condemned the lack of courage by influential people as “worse than the ravings of the militants”.
Her attack comes a week after a landmark report warned gender-questioning children should be steered away from medical treatment.
The Cass review found kids have been “let down” by the NHS and it called for gender services for young people to “match the standards of other NHS care”.
Writing in The Sunday Times, Ms Badenoch said: “In the case of trans ideology, those who first publicly questioned its tenets were subjected to hysterical abuse and calumny.
“Worse than the ravings of the militants was the cowardice of those in positions of influence.
“How many university administrators, media editors, police officers, politicians preferred to keep quiet for fear of becoming the next target?”
She went on: “Had those who warned gender services in the NHS had been hijacked by ideologues been listened to instead of gagged, kids would not have been harmed and the Cass review would not have been required.”
Dr Hilary Cass concluded young people have been caught up in “stormy social discourse”.
Prime Minister Rishi Sunak said it shows the need to “exercise extreme caution” in gender care.