The First Minister voiced her disagreement in response to a tweet posted by the Harry Potter author.
The long-awaited Gender Recognition Reform (Scotland) Bill was tabled at Parliament on Thursday as MSPs were urged to take a ‘respectful tone’ during considerations of the reform.
Obtaining a gender recognition certificate means a trans person is legally recognised in their acquired gender, and can obtain a new birth certificate showing that gender.
The existing gender recognition process means applicants have to be medically diagnosed as having gender dysphoria, go through a minimum two year process and be aged over 18.
The reforms mean trans people would no longer need to provide medical reports or evidence, and the process would be quicker and made available to those aged 16 and over.
In a tweet, Rowling said: "The law @NicolaSturgeon's trying to pass in Scotland will harm the most vulnerable women in society: those seeking help after male violence/rape and incarcerated women.
"Statistics show that imprisoned women are already far more likely to have been previously abused.”
Ms Sturgeon posted that she “fundamentally disagreed”, when asked if she agreed with Rowling over whether the reform “will harm the most vulnerable in society”.
The Firs Minister said she had not read the tweet, but claimed Rowling was “clearly free to express her opinion”.
She said: “This is about an existing process by which people can legally change their gender and it’s about making that process less traumatic and inhumane for trans people – one of the most stigmatised minorities in our society."
Ms Sturgeon added: "It doesn’t give trans people any more rights, nor does it take away from women any of the current existing rights under the Equality Act.
"There was a plea [in Parliament] to have a debate that was civilised, that was respectful of different opinions, but that didn’t give inadvertently sucker to those – and I’m not describing anybody like JK Rowling or anyone else in this way for the avoidance of doubt – to exploit this issue for purposes of prejudice and transphobia.”