Kate Forbes has said she would have rebelled against Nicola Sturgeon's flagship gender reform plans in their current form.
The finance secretary was on maternity leave when a majority of MSPs voted in favour of the Gender Recognition Reform (GRR) bill in December last year.
Forbes, who announced her decision to stand for the SNP leadership today, said she had "significant concerns" about the legislation.
The bill, which was intended to make it easier for people to legally change their gender identity, was a key part of the Scottish Government's legislative agenda.
But the UK Government issued a rare Section 35 order to block the Holyrood bill from becoming law, claiming it would negatively impact on existing equalities legislation.
Forbes said she would be "loath to challenge" that decision. She told BBC Scotland: "I understand the principle here which is that the UK Government should not overturn Scottish legislation.
"That is an important principle which I hold to. But I think on this, seek legal advice and recognise it is not a priority right now for the people of Scotland, who are focused on other things."
Her stance puts her at odds with Humza Yousaf, who is considered the front runner in the race to become the next SNP leader.
Speaking at a campaign event in Clydebank today, the health secretary said that "progressive" SNP policies like gender reform had brought the party within "touching distance" of achieving independence.
Under parliamentary convention, Forbes would have been expected to resign from the Scottish Government Cabinet if she had voted against one of its principal policies.
There was speculation the bill had been rushed through Holyrood before the finance secretary was due to return from maternity leave in April.
She said: "That would have been a question of collective responsibility and that would have been a decision that I would have had to take in discussion with colleagues. Obviously I wasn't there."
Forbes added: "Well, I didn't predict the date at which my daughter would be born and neither did I set the government's timetable so it is certainly nothing that I had control over.
"But I have concerns about self id and those concerns remain."
Forbes is a committed member of the Free Church of Scotland which is known for its socially conservative views.
Asked by the BBC if a man should be able to marry another man, she added: "Equal marriage is a legal right and therefore I would defend that legal commitment.
"Incidentally though I would hope that others can defend the rights of other minorities, including religious minorities that might take a different view."
Forbes insisted there was a distinction to be made between personal morality and practice.
She added: "In terms of the morality of the issue I am a practicing Christian and I practice the teachings of most mainstream religions - whether that is Islam, Judaism or Christianity - that marriage is between a man and a woman.
"But that's what I practice. As a servant of democracy in a country where there is law I would defend to the hilt your right and anybody else's right to live and to love without harassment or fear."
Forbes had earlier shared a video on social media announcing her intention to stand for the leadership.
She said: "More than anything, we need a leader who is bold, brave and energised, fresh-faced and ready for new challenges
"Somebody who inspires your confidence as an SNP member and who inspires the confidence of the people of Scotland to vote for a better future.
"I am that leader and I want to lead our party into better days with integrity and commitment for the sake of your children and my children."
Yousaf had earlier faced questions earlier about the relationship between religious beliefs and politics.
"I’m a person of faith myself," he said. "I’ll be fasting during Ramadan in a number of weeks’ time but I don’t legislate based on my faith. That is not, I think, the job of elected representatives.
"Our party has done well being a socially progressive party and I want to make sure we continue to go down that route."
Several of Forbes' SNP colleagues defended her over her Christian faith and membership of the Free Church of Scotland.
Glasgow MP Carol Monaghan said it was "incredibly disappointing" to see Forbes "targeted" over her faith.
She added: "Having the courage to stand by her beliefs can only be a positive for the role of First Minister".
Ash Regan, the third contender for the SNP leadership, said: "I am utterly appalled by the misogynistic attacks on Kate Forbes because of her faith.
Kate is and always will be a great friend and colleague and it distresses me to witness this. It must stop immediately."
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