Scotland’s equalities secretary has reaffirmed the SNP government’s commitment to transgender rights, while insisting that those raising genuine concerns about a conflict with women’s rights “shouldn’t suffer knee-jerk accusations of transphobia”.

Shirley-Anne Somerville’s comments come after the party was asked to clarify its stance following the leak of private messages between three prominent female MSPs that claim the first minister, Nicola Sturgeon, is “out of step” with her party.

Somerville acknowledges in a blog written for the Scottish government’s Fairer Scotland website that discussion of transgender rights has become “very polarised”, but concludes that “trans men and women are amongst the most stigmatised groups in our society. They deserve to know that their government is working to change that.”

Somerville writes: “Just as the first minister has herself said in the past, I personally don’t feel conflict between my support for trans rights and my support for women’s rights. But I know that some do feel that conflict – and that the issues they are raising are not motivated by transphobia but by a concern, sincerely felt, that space hard won by women down the generations will be compromised.”

In the leaked conversation between Ruth Maguire, who is the convenor of Holyrood’s equalities and human rights committee, the Aberdeenshire East member, Gillian Martin, and the community safety minister, Ash Denham, the SNP MSPs discuss worries that the first minister is not aware of their concerns regarding transgender rights reform “because no one has conveyed [MSP] group feelings to her”.

The SNP government has promised to radically reform the Gender Recognition Act 2004, such as by allowing individuals to change their legal gender through self-declaration. But the proposals were not included in last autumn’s programme for government, and the director of Stonewall Scotland, Colin Macfarlane, on Wednesday called on the Scottish government to publish its response to the consultation on the proposals, stating: “It’s been over a year since the consultation closed. The lack of response is causing real anxiety among trans people.”