In a directive issued in November last year, Archbishop Hart asked Catholic school principals and parish priests to conduct confessions "in an open setting in the full view of all participants, who are supervised by staff".

The parish priest must ensure there is a "direct line of sight" to the penitent.

But there is debate about what constitutes an "open setting" and how much privacy students and priests should be given during confession.

And one priest has defended his decision to continue using the confessional box for students at St Augustine's Primary School in Yarraville.

Father John O'Connor, has argued that this does not violate the Archbishop's call, as the child's door remains open, allowing for teacher supervision.

Archbishop Hart said while canon law "requires" that confessions occur "with a fixed gate between the penitent and the confessor, it also allows for confessions to be heard outside a confessional under special circumstances".

The letter described Victoria's new child safe standards as "special circumstances".

In February, all five metropolitan Archbishops told a hearing of the federal child abuse royal commission that they would endorse a national standard that removed the use of confessional boxes for children.

When Father O'Connor hears primary school student confessions in the traditional booths, he keeps the child's door open, but keeps his own door shut.

Father O'Connor said the child "is always in clear view of the other children in the church and the teacher".

He said the confessionals were important because they gave students privacy.

"The church has been in this game for a long time and it knows what is best for the penitents.

"Anonymity makes it easier for them to unburden themselves with anything in regard to sin," he said, noting that he had not been challenged about the confessionals in nearly 19 years as a priest.

While there is no suggestion that Father O'Connor poses a risk to students' safety, child safety experts are asking priests to do away with confessional boxes when interacting with young children.

Australian Childhood Foundation's chief executive Joe Tucci said best practice was to avoid enclosed spaces and secret interactions between adults and children.

"It's not about the religious virtue of it, I'm not against children talking to priests about things, but I do believe that we should be encouraging and modelling to children that anything that promotes secrecy isn't a helpful orientation," he said.

Dr Cathy Kezelman, president of Blue Knot Foundation, which supports child abuse victims, said even if the door of the child's confessional booth was open the room was still a "closed dark space".

"A lot of work is being done to make institutions and all aspects of institutions safe for children, where there can be transparency and visibility, and this would appear to be flying completely in the face of that."

President of the Victorian Association of Catholic Primary School Principals, Michael Gray, said confessions of students at his school, St Joseph's Primary School in Warrnambool, were heard on the altar, where it is "open in front of the congregation".

However Kate Drane, who is on the school's parents committee, said she supported the use of the booths.

"The children are never unattended, at any time," she said.

"I have faith in our school and our parish."

According to the Catholic Archdiocese of Melbourne's spokesman, Shane Healy, the confessionals may be "old fashioned" but the Archbishop's directive was "being upheld" in Yarraville, as the child's door was open.

"The priest is behind closed doors, there is a thick wall between himself and the penitent, and the door of the child is completely open and in full view of all other students and any teachers or parents who are on hand," he said.

A spokesman for the Catholic Education Melbourne spokesman and St Augustine's Primary School said they believed the school and parish "abide" by the Archbishop's statement.