The First Minister refused to back down after labelling some opponents transphobic, homophobic, misogynist and “possibly” racist too. However, she said this did not apply to the majority of critics.
Ms Sturgeon sparked a row last week after saying there were those who oppose the reforms "that cloak themselves in women's rights to make it acceptable, but just as they're transphobic you'll also find that they're deeply misogynist, often homophobic, possibly some of them racist as well”.
The Scottish Conservatives called the comments “disgusting and desperate”. Author JK Rowling, a prominent critic of the plans, also criticised them on Twitter.
MSPs passed the Gender Recognition Reform (Scotland) Bill by 86 votes to 39 before Christmas, approving reforms which would allow trans people to obtain a gender recognition certificate (GRC) without the need for a medical diagnosis.
The Bill would also allow 16 and 17-year-olds to apply for a GRC for the first time, and would reduce the amount of time a person has to live in their acquired gender before they can be granted the document.
The UK Government has since moved to block the reforms, raising concerns about their UK-wide impact. Meanwhile, a separate row has broken out over the treatment of trans prisoners in Scotland.
Speaking to journalists during a visit to BBC Studioworks’ new multi-camera television studio at Glasgow’s Kelvin Hall, Ms Sturgeon said: "It is not the case that everybody who opposes this legislation is badly motivated, and I don't believe that. I'm not even saying the majority are.
"But I think anybody who looks at this debate will also see that there are people who attach themselves to this debate who are also against rights for women and rights for gay people."
The First Minister added: "I don't think I've said anything there that is not obviously the case. And I think it actually does help to separate those who are using the trans debate as a way to row back on rights for others, from the very real concerns that have been expressed."
Ms Sturgeon said she abhorred and condemned abuse directed at anyone on either side of the debate, adding: "I know how tough that is, because I've probably had more abuse hurled at me on this issue than any issue in my time in politics."
She said her language was never intended to be inflammatory.
Earlier, talking to broadcasters, Ms Sturgeon was asked who she was referring to when she labelled some critics bigots.
She said: "Look, I'm not naming individuals, and I was very clear to say that many of the concerns raised about the recent legislation are real concerns and I'm not in any way suggesting opponents of that legislation are by definition badly motivated.
"But everybody is aware that in this debate, and it always has been the case and is the case in many countries, some people who are anti rights for trans people are probably anti rights for gay people and other minorities as well. That is a fact."
Pushed on the issue, Ms Sturgeon said: "I don't think you have to look very far, and I think most people can see – even opponents of this legislation, I think, would accept that there are some people who will argue against rights for gay people, they will argue in other contexts against rights for women. I was making the point that there are people who have decided to become so-called advocates for women's rights on this issue who have never stood up for women's rights before."
She added: "I'm talking in general terms, and I actually don't think that it's something that is capable of being denied in any real sense."
Asked if she thought Rowling was transphobic, Ms Sturgeon said: "No."