ANAS Sarwar has accused the Scottish Greens co-leader Lorna Slater of polarising the transgender debate and using language that "pushes people to extremes".
The Scottish Labour leader said comments by Ms Slater were "very, very unhelpful".
She recently sparked a row after drawing parallels with people she regarded as having “anti-trans” views to racists and anti-Semites.
Critics accused her of equating “those who have legitimate concerns over the impact of this legislation on women’s rights and safety with racists” and said her remarks arguably amounted to a breach of the ministerial code.
Ms Slater and fellow Scottish Greens co-leader Patrick Harvie are both ministers in the Scottish Government following a co-operation agreement with the SNP.
Speaking to The Scotsman, Mr Sarwar said it was “very easy for Lorna Slater and the Greens to think that the twittersphere or social media represents the real world”.
He added: “I think that there are lots of people who are well-intentioned, who want us to come to a sensible place that recognises the need to protect women's rights and also at the same time give greater protections to people who are the victims of transphobia.
"I think to polarise the debate in the way that Lorna Slater has done, I think is very, very unhelpful and pushes people to extremes in a way that is unnecessary."
Nicola Sturgeon backed Ms Slater last week, accusing critics of misrepresenting her minister's comments.
The First Minister had been urged to launch an official investigation into claims Ms Slater broke the Ministerial Code in the language she had used.
Ms Slater, who is the Scottish Government’s Minister for Green Skills, Circular Economy and Biodiversity, was described by one Tory MSP as a “radical extremist”.
At least three complaints were sent to the First Minister over the comments made in an interview with the Herald on Sunday.
In her interview with journalist Neil Mackay, Ms Slater said that the BBC had only recently stopped giving a platform to climate-change deniers because they required balance. “We wouldn’t put balance on the question of racism or anti-Semitism, but we allow this fictional notion of balance when it comes to anti-trans [views]. The whole thing is disgusting," she said.
The minister also claimed that some of the opposition to the reform was being funded by money “from certain right-wing American groups that’s been flooding into organisations in the UK”. Feminist groups have rejected her claim.
The Scottish Government is seeking to reform the Gender Recognition Act to simplify the process for a trans person to legally change their gender.
Current rules require individuals to obtain a medical diagnosis and spend a minimum of two years living as their chosen gender.
Supporters say the move will streamline a process many find distressing, but critics have raised concerns self-identification will undermine women’s sex-based rights, such as access to women-only spaces.
Mr Sarwar said it was "undoubtedly” a difficult debate featuring “strong opinions”.
He said: "We've got to protect sex-based rights, and at the same time we've got to make sure we're counteracting transphobia.
"And I've never been the kind of politician that likes to pit community against community or minority against another minority, or minority against majority even, in some cases.
"It's about how we build understanding, but we do so in a way that we go through the legislative process, so we have a robust piece of legislation that challenges the complexities but also busts some of the myths, and we do it in a way that we can build a fairer, more equal society at the same time, and not pitting community against community."
Asked if his party will allow a free vote on the issue in Holyrood, to avoid repercussions if MSPs go against the party whip, Mr Sarwar said he hoped “we can try and find a form of consensus”.
A spokesman for the Scottish Greens said: “Mr Sarwar has deliberately misinterpreted what was said, which was about the nature of discourse in the media.
"The Scottish Greens are clear that discussions surrounding gender recognition reforms must be respectful and free from bigotry which denies the existence of trans people or portrays them as predators.”
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