Catholic Archbishop Paul Martin accepts that survivors of abuse want the church to take responsibility and not just leave it to a particular order that may have been involved.
He made the comment at the Abuse in Care inquiry investigating historical abuse by the St John of God Order at Marylands School in Christchurch.
The order ran the school between 1955 and 1984.
Archbishop Martin said the culture at the time was wrong.
He is the former bishop of Christchurch, and now Coadjutor Archbishop of Wellington.
He still administers the Christchurch Diocese awaiting the appointment of a new bishop.
When an order, such as St John of God, works in a diocese it is done with a bishop's permission, but lines of control become blurred.
Archbishop Martin said bishops cannot be closely involved in everything going on in their diocese and that religious orders were set up to do the work.
"The idea that he had oversight of it all is not quite the reality. It wasn't really their expectation either from the bishop.''
Martin said the bishop at the time believed that in bringing the St John of God brothers to Christchurch to care for young people he was setting up something that would meet their needs.
''It was the handing over in good faith and good belief that they would do what they said they would do. As it turns out that wasn't the case."
He is much more confident now that the Catholic Church has better structures in place to oversee work going on in its name.
''Any new works that are set up now are much more prescribed in terms of what is expected, the reporting. If an order was to come in and do something I expect we wouldn't just be leaving it to them in the way that happened in the past.''
Royal Commission chair Coral Shaw put it to Archbishop Martin that evil was being done at Marylands and it was known at the time by some within the church.
Judge Shaw asked him if it was ever right to cover up the abuse and ignore it, to which he replied no.
Shaw put it to Archbishop Martin that it was always the responsibility of the bishop and every other religious person who knew about the abuse to do something
''It was, yes,'' he said.
Martin said the right thing was not done all of the time.
Shaw said that for decades the bishops of Christchurch knew that things were going on, but things were not right.
Martin agreed with Judge Shaw that brothers at Marylands who offended against children should have been removed straight away.
''I think that was the culture of the time and it was wrong and we have the results and the fruits of that and what a terrible legacy for us to carry as a church, as a society.''
Judge Shaw went on to ask the Archbishop if he accepted that the Catholic Church as a whole should take responsibility for the healing and redress for survivors.
''They are not concerned about the niceties on whether this is a religious (order) or a diocese. Whether it is a bishop or a provincial. They want to be healed.'
''Do you think the Catholic Church in New Zealand is prepared to step up and do it part towards that?", she asked.
''I hope so and this is why we asked to be part of this (the Royal Commission process) and we knew that in doing that we were coming with all our history and our past, so as a bishop and one for the future, I am saying, yes.''
Archbishop Martin had earlier in the hearing on Wednesday apologised to survivors of Marylands.
He said it brought deep shame and sorrow and that their stories of abuse broke his heart.
The Royal Commission hearing into the St John of God Order ends on Thursday.