In an embarrassing U-turn, the Melbourne Archdiocese has removed Father Tom Knowles from one of the nation's busiest churches just weeks after reinstating him.

The move comes after revelations by Fairfax Media last month that a confidential church inquiry had found he had an improper sexual relationship with disabled woman Jennifer Herrick for 14 years in NSW.

As a result of this inquiry, Father Knowles was put on administrative leave for 16 months but was returned to active ministry in January.

His reinstatement was criticised last month by Ms Herrick and victims' groups, especially in light of a confidential letter from the church to her acknowledging ''the harm that can be caused to vulnerable people in such a case''.

Last month, senior church official Father Graeme Duro defended Father Knowles' return to active ministry at St Francis' Church in Melbourne's CBD, stating that the priest had taken "responsibility for his actions … and it is appropriate for him to return to public ministry''.

But in the past fortnight, other senior church officials have intervened in the case and have had Father Knowles removed.

Church documents obtained by Fairfax Media this week reveal that Melbourne Archbishop Denis Hart has formally withdrawn Father Knowles' "faculties to engage in any public ministry within the jurisdiction of the Archdiocese of Melbourne".

Archbishop Hart is understood to have received letters from concerned Catholic parishioners after Father Knowles' reinstatement was made public.

Ms Herrick said that while she ''believed it was just'' Father Knowles had been stood down, she was ''still incredulous'' she had not been told about it immediately by the church. Ms Herrick was 19 and suffering from bilateral congenital hip dysplasia - which caused her to walk with an abnormal gait - when Father Knowles, who was then her family priest, began cultivating a relationship with her and her extended family.

Three years later, the priest initiated sexual intercourse with Ms Herrick, who had never had sex before. The sexual relationship continued for 14 years and Ms Herrick later described it to church investigators as abusive and exploitative conduct.

''Archbishop Hart was overseas when I formally communicated to him in early January the decision to return Father Knowles to ministry,'' Father Duro said.

''On the return of the Archbishop, I met with him and he advised me of his decision to remove the faculties from Father Knowles from public ministry … There is no present intention for Father Knowles to engage in public ministry.''

Ms Herrick has received no payment for media contact regarding this issue. She hopes other women will have the courage to tell their own stories.