Sister Ellen Flynn, head of the Daughters of Charity of Saint Vincent de Paul in the UK, told the Scottish Child Abuse Inquiry the congregation had “failed to engage” with the complaints about Smyllum Park orphanage in Lanarkshire when they first emerged in 1998.
Sister Flynn broke down as she expressed regret for the abuse suffered by children at the orphanage, saying she had been “torn apart” by the evidence heard by the inquiry.
But she said the order had failed to “pursue” allegations of abuse in the late 1990s because of advice from solicitors that legal action would be time-barred.
MSPs last year passed legislation removing a three-year time bar which had been previously prevented those bringing civil claims relating to child abuse.
Sister Flynn accepted abuse had taken place at Smyllum and said the order was carrying out work to establish the names of former child residents buried in an unmarked grave at nearby St Mary’s cemetery in Lanark.
The inquiry has heard allegations from former residents of Smyllum that children were beaten, force-fed and humiliated for wetting the bed by being made to wear soiled sheets.
Trainee priests and a man later convicted of sex offences against children, Brian Dailey, were allowed unsupervised access to the children at the orphanage, which closed in 1981.
Dailey was jailed for ten years in July after being found guilty of physical and sexual offences against children in the 1970s and 80s, including at the now-closed Ladymary residential school in Colinton, Edinburgh.
Sister Flynn, who gave evidence alongside Sister Eileen Glancy, said the sisters were “deeply sorry and distressed” by what they had heard during the course of the inquiry.
She broke down as she said: “For any child that has been abused while in our care, we would feel a very, very deep sense of regret for the long-lasting effect on that person.
“There’s so much more being said and many more people coming forward. All of this is totally alien to us – we’ve been torn apart.
“These were our children and we were supposed to be taking care of them, but I also want to stand by our sisters who say this was a happy place.”
Sister Flynn said the congregation now wanted to “affect healing” for all those who had suffered.
“What we want to do is what we didn’t do before in the 1990s," she said. "We want to engage with it...”
The inquiry heard that 122 allegations of abuse were made between 1998 and 2000 but while one civil case was taken to a preliminary hearing, it was found to be time-barred due to the number of years which had passed since the abuse was alleged to have taken place.
Earlier, Sister Glancy said the congregation was at a “complete loss” over what happened to the medical records of former residents and personal records kept by nuns who worked at Smyllum.
Asked by Colin MacAulay QC, lead counsel to the inquiry, if the records had been destroyed, she said: “I think they must have been because they are certainly nowhere in any of our establishments. I presume they must have been destroyed.”
The inquiry heard how the deaths of children or attempts to run away should have been reported to the Secretary of State, but nothing has been found in the archives to indicate this took place.
The inquiry has previously heard how former resident Sammy Carr, 6, died of a brain haemorrhage in 1964 as a result of an E.coli infection probably contracted from playing with a dead rat.
Another child, Patricia Meenan, 12, died after being hit by a car while attempting to run away from Smyllum in 1969, while Francis McColl died in 1961 aged 13 after accidentally being struck on the head by a golf club.
Asked about the deaths, Sister Flynn said there had been a lack of internal systems and governance “across the board”.
Speaking after the hearing, Alan Draper, a spokesman for In-Care Abuse Survivors (Incas), said: “We heard today that the Daughters of Charity have accepted responsibility for failing to have proper abuse procedures in place; for not investigating allegations of abuse and for not referring the allegations to children services and police.
“The acceptance of responsibility is despite the previous denials that any such abuse took place. This is a devastating admission by the order and vindicates the evidence given my many witnesses to the abuse. The order has followed the pattern set by the Catholic Church by at first denying the allegations, then seeking to minimise the abuse, and then seeking to blame the victims.
“Those organisations will no doubt seek to state that they were following the advice of lawyers and insurance companies, whose primary role would be to minimise the potential financial damage to the organisations for their failures. These failings put the reputation and the needs of the organisation before vulnerable children.”
The inquiry, led by Lady Smith, continues.