It comes after prison chiefs in Scotland in recent weeks approved moving Tiffany Scott, who stalked a 13-year-old girl while known as Andrew Burns, to an all-female prison.
Last week, Nicola Sturgeon said that Isla Bryson, a transgender woman convicted of rape carried out while she was a man, will not be imprisoned in the all-female Cornton Vale prison in Scotland.
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.”