The head of the St John of God Order in Oceania has denied that a lack of documents relating to historical allegations of abuse at Marylands School was a cover-up.
The Order ran Marylands, a boarding school in Christchurch for boys with learning disabilities, between 1955 and 1984.
It is under investigation by the Abuse in Care inquiry.
Numerous complaints have been made over the years and two members of the order were jailed for sexual crimes against boys in their care.
Brother Timothy Graham began his appearance on Tuesday, on audio-visual link from Sydney, with an apology to survivors.
''The fact they were places of sexual, physical and psychological abuse is horrific and indefensible.''
He said he understands and shares in their anger.
''The thing that disturbs me is a sense of betrayal of those vulnerable young people.''
Brother Graham told the inquiry that while he had no personal insight on the high level of sexual offending at Marylands, he did have a theory.
''It may be as a closed system, as it was in those days, where there was not much oversight from outside the organisation, that could account for it. I think if we look at it in modern scenarios, there's a lot of accountability, there's a lot of transparency, there's a lot of outside auditing of services these says, which just didn't happen in those days.''
The hearing was told there is a lack of documentation concerning allegations of abuse made to St John of God.
Brother Graham dismissed claims of a culture of not keeping adequate records.
''In our archives those documents aren't there. Not that there was a culture of not recording. I don't support the notion from my practical experience and knowledge that there was a practice of not recording.''
Commission Chair Coral Shaw said a lack of documentation made it very difficult to find out what was known and at what stage.
Brother Graham agreed with that.
The lawyer assisting the Commission, Katherine Anderson quizzed Brother Graham on evidence about a reference in a letter from the then head of the Order in New Zealand, that it was best to destroy any anonymous letters alleging abuse because of the harm it could do.
''Do you accept that is a cultural practice within the order not to record matters because it could harm a brother?''
Graham said he did not accept that.
''I accept that this was an appalling lack of judgement. Should never have occurred. The letter should have been kept. The existence of the letter only came to light because the man informed the police himself. It is not good practice. Doesn't look good and should never have happened.''
Legal advice to the Order in the early 2000s was cautioning against cases going to open court because it could mean the discovery of documents .
''Concern expressed about the possibility of exemplary damages due to the gravity of the abuse, and there is evidence that the possibility the abuse was brought to the notice of the Order previously and not acted upon,'' Anderson said.
Graham responded that it was preferable to mediate, rather than go to court.
''Not re-traumatising victims having to go through a court case. A whole lot of reasons that the two sets of lawyers would be discussing with each other. With each other I would hope to minimise the trauma that would be placed on people who are already struggling to deal with the traumas of the past.''
Graham said survivors need to chart their own journey through the process, because only they know what they want.
He was asked to comment on the Order caring for brothers and ex-brothers who have had allegations made against them or been convicted.
''I am in a difficult position as the Provincial (head of order in Australia and New Zealand), as a religious, as a christian. I am clearly held and wish to support people who have been harmed, but unfortunately we are also required to support people who have done the harm. That is a very difficult position to be in.''
He refuted a claim made on Monday by Clinical Psychologist, Michelle Mulvihill who said the Order was in organisational denial suggesting the Order does not acknowledge the impact this harm has had on its victims.
''The brothers feel the pain and anger of the victims very deeply. Personally, daily I feel the sorrow and shame for what was done to these vulnerable young people and it has just been reinforced by listening to their evidence during this Royal Commission.''
''To claim we are in denial and don't care I think is grossly unfair and grossly unsubstantiated. We know how we feel. We feel very deeply about this.''
On Wednesday, the police will give evidence on its investigation into Marylands School.