It comes after Isla Bryson was taken to a female-only prison following her conviction of two rapes which took place when she was a man.
The Scottish Prison Service has paused the movement of all transgender inmates while it carries out an “urgent review” of its rules.
It comes after Tiffany Scott, who stalked a 13-year-old girl while known as Andrew Burns, requested a transfer to a women’s prison, which was reportedly approved.
In a separate case, Isla Bryson was earlier this week taken to a female-only prison after being convicted of two rapes which took place when she was a man known as Adam Graham. She was later transferred to a prison on the male estate, understood to be HMP Edinburgh.
Scotland’s Justice Secretary announced a pause on its transgender prison rules after MSPs voiced anger at reports that prisoner Ms Scott’s request to move to the women’s estate had been rubber stamped.
After Bryson’s case was raised at First Minister’s Questions, Nicola Sturgeon said the prison service carried out individual risk assessments in such cases and no “formal direction” had been given by the Scottish Government.
In a statement, the Justice Secretary said the measures would be in place until the Scottish Prison Service completes a review of its management of trans prisoners.
Mr Brown said: “I understand that the issue of any trans woman being convicted of violent and sexual offences is a highly emotive subject and that the public concern is understandable.
“As the First Minister pointed out last week, we must not allow any suggestion to take root that trans women pose an inherent threat to women.
“Predatory men are the risk to women. However, as with any group in society, a small number of trans women will offend and be sent to prison.
“Therefore, I hope that the measures I am about to highlight will offer reassurance in the ongoing ability of the prison service to manage trans individuals and ensure the safety of all prisoners.
“We must also never forget that there are victims in these cases. My thoughts remain with them.”
He introduced two rules, the first being that no transgender person already in custody with any history of violence against women will be moved from the male to the female estate.
The second is that no newly convicted or remanded transgender prisoner with a history of violence towards women will be placed in the female estate.
Mr Brown continued: “It is important to be clear, however, that SPS policies have in no way been changed or impacted by the recent passing of the Gender Recognition Reform Bill (which, in any event, is not yet in force).
“SPS have already been undertaking, in dialogue with the Scottish Government and other stakeholders, a review of the management of trans prisoners, which is nearing completion
“In addition, an urgent lessons learned review has been instructed in relation to the case of Isla Bryson, with any learning to be applied immediately to existing transgender cases in the prison estate.”