In a blog on the Scottish Government's website, Ms Somerville appealed for the polarised debate about transgender rights to become more respectful.
She said that she was a "trans-ally" but that many women feel that "space hard won by women down the generations will be compromised" if proposed changes to the Gender Recognition Act are approved.
The law change would mean that transgender people would be able to "self-declare" their gender - rather than having to have a medical diagnosis of gender dysphoria. There have been concerns raised that this could erase women's sex-protected rights.
Ms Somerville said she believed that there was "not so much a problem with the rights of trans women but instead a fear of men who abuse women."
Her blog was praised today on Twitter by Nicola Sturgeon who said: "As both a #TransAlly and a proud feminist, I want us to understand and address the concerns being expressed, so we can build a Scotland where everyone feels safe and secure."
The First Minister's tweet, and the blog post, come a day after a private conversation between three female SNP MSPs, in which they criticised Ms Sturgeon's stance on transrights, was leaked.
Gillian Martin, Ash Denham and Ruth Maguire also alluded to a meeting Ms Somerville had with the SNP group where concerns were expressed about government support for proposed changes to the Gender Recognition Act.
In her blog, Ms Somerville appeals for the "polarised" debate around transgender rights and women's rights to become more respectful, and says it is her "duty" to try and encourage that.
She writes: "I am a strong supporter of trans rights and equality. I have met too many trans men and women, particularly young people, who struggle on a daily basis just to feel safe, secure and accepted for who they are, for me to be anything else.
"The hurdles they face and the damage they often suffer is immense. I want Scotland to be a place where we work to put that right, a country where they do feel safe, secure and accepted. So, I have no hesitation in calling myself a trans ally – and I hope trans women and men see me that way too."
She adds: "But I am also a woman and a lifelong, passionate feminist – and I know that while the battle for women’s rights and equality has made great strides in recent years, there is still much more to do. I also know that, at times, the progress already made can feel fragile.
"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."
Ms Somerville goes on to say there has is a danger in "over-simplifying complex issues" but that at the core of some concerns raised "it is not so much a problem with the rights of trans women but instead a fear of men who abuse women. The fear is that some men will use trans equality as a Trojan horse to access women and do us harm."
She adds: "I understand that. But it means the problem we face is not one of trans women wanting to feel safe and accepted – it is one of how we protect and safeguard women against potentially abusive men. That’s not a new problem in Scottish or global society – nor is it one created by trans women."
"If we are able to appreciate this and other perspectives, I believe we can work through many of these issues, address the concerns that are being raised, and make Scotland a place where everyone can feel safe. And do so while standing full square behind the rights of trans men and women not to be discriminated against."
There is no reference in the blog to the leaked conversation of the three SNP MSPs, or to the online abuse that SNP MSP Joan McAlpine has also received since she has publicly spoken out about the impact on women of the GRA and a conflation of sex and gender.
But Ms Somerville says: "people raising genuine concerns about women’s rights shouldn’t suffer knee jerk accusations of transphobia. However, it is also impossible to deny that there is a considerable degree of transphobia in our society.
"I hope, therefore, that – whatever views any of us may hold on the relationship between trans rights and women’s rights – we will all unite against transphobia, just as we do against homophobia and any other form of prejudice and discrimination.
"Trans men and women are amongst the most stigmatized groups in our society. They deserve to know that their government is working to change that."