The prison service will carry out an urgent review after trans rapist Isla Bryson was placed in a women's jail.
He said an "urgent review" into the case of a trans woman convicted of raping two women before changing gender will also be carried out.
There was a public outcry when Isla Bryson was initially remanded to Cornton Vale women's prison.
She was later moved to a men's jail.
Further concerns were raised by the case of Tiffany Scott, previously known as a man called Andrew Burns, who had an application to move to a women's prison approved.
She has a history of violence and is serving an order for lifelong restriction, meaning she will only be released when she is no longer considered an "unmanageable risk to public safety".
Critics argued vulnerable women prisoners, many of whom were victims of male violence, were being placed at risk.
Justice Secretary Keith Brown said the "urgent lessons learned review" into the Bryson case would be completed by Friday.
The prison service was already undertaking a wider review of its transgender policy, which will continue.
Until that ends, Mr Brown said:
* No transgender person already in custody with a history of violence against women will be moved from the male to female estate
* No newly convicted or remanded transgender prisoner with any history of violence against women (including sexual offences) will be placed in the female estate.
Any exceptional cases will require the approval of Scottish ministers, he said.
Bryson was convicted of rapes carried out while she was known as Adam Graham
"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," Mr Brown said.
"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.... will offer reassurance in the ongoing ability of the prison service to manage trans individuals and ensure the safety of all prisoners."
The move is likely to affect only a small proportion of inmates - about 0.2% of the total prison population in Scotland.
According to the latest Scottish Prison Service statistics, there were 11 trans women, four trans men and three non-binary/gender fluid prisoners between July and September 2022.
There were 7,092 male prisoners and 280 female inmates.
The Scottish Prison Service (SPS) has previously said the decision on where to accommodate transgender prisoners was taken on a case-by-case basis, after thorough risk assessments.
Mr Brown said it was vital that this continued.
An SPS spokesperson confirmed the urgent review had begun.
They said the review would consider any history of violence or sexual offending against women, and any associated risk they pose.
"Until the review is completed, any trans individuals, with a history of violence towards women, will only be admitted to the male estate, in segregation, when they first enter our care," they added.
"This arrangement will be progressed in line with our human rights obligations.
"Finally, our ongoing policy review will be independently assessed by experts in women affected by trauma and violence."
Cornton Vale women's prison is due to close soon, to be replaced by a new jail - HMP Stirling
Scottish Conservative MSP Russell Findlay said: "After much dithering and flip-flopping, the SNP government has finally been shamed into doing the right thing.
"Just days ago, the justice secretary tried to pass the buck, saying decisions on trans prisoners were for the Scottish Prison Service.
"But as public anger escalated, Nicola Sturgeon was forced to intervene by ordering the removal of a double rapist from a women's prison.
"It should not have taken a second shocking case for them to ban all transfers. The long overdue SPS policy review must now be completed as a matter of urgency."
He called for a full investigation by Holyrood's criminal justice committee to investigate how Bryson ended up in a women's prison.
Scottish Labour's justice spokeswoman Pauline NcNeill said: "The safety of women and women prisoners is of paramount concern, and it's welcome to see Mr Brown finally recognise that.
"The SNP have been aware of the failures of the current policy in this area since it was agreed in 2014, it should not have taken this level of public outcry to do the right thing.
"The Scottish government now needs to change the policy which they oversaw and to bring forward guidance which take account of the views of woman prisoners as a matter of urgency to make sure this does not happen again."