Transgender prisoners will be able to choose whether they go to a male or female prison.
Corrections Minister Anne Tolley says changes are being made to prison regulations so any transgender prisoner whose birth certificate has not been changed can apply to be moved into a prison with their identified gender.
This option excludes any prisoners facing or serving sexual offence charges.
Currently nine transgender offenders are in jail.
Meanwhile, remand prisoners will no longer all be treated as high security offenders.
There will be individual security assessments and those who are not deemed to be a high security risk will have more access to rehabilitation programmes.
Another change allows Corrections' staff more options around restraining a prisoner to protect them from self-harm.
Northland lawyer Kelly Ellis represented Whangarei transgender Glen Cooper who was convicted on a serious assault charge last year but sent to a men's prison, despite telling the court she suffered continual sexual assault when locked up with men.