The outgoing head of Presbyterian Support Otago says the abuse in care inquiry has taken a toll on her.
The organisation said Jo O'Neill had made the personal decision to step down after almost five years of service.
The Royal Commission of Inquiry into Abuse in Care revealed that Presbyterian Support Otago (PSO) destroyed records of children in its care in late 2017, before the commission began its inquiry.
The report said the organisation's chief executive at the time, Gillian Bremner, told a staff member to destroy the records, apart from a register of names and dates.
Bremner told the Inquiry she obtained advice from lawyer and ex-Presbyterian Support Otago Board chairperson Frazer Barton about destroying the records.
O'Neill, who stepped in as chief executive in 2019, told RNZ she did not know why the records were destroyed, but it was not something she would do.
"All I am aware of is that a staff member at the time, who is no longer here as well, was informed the destruction of the records was to occur," she said.
"At the end of the day, all I can say is that I am heartbroken that those records were destroyed. I am completely appreciative of the fact that it would've enabled individuals who had been on a journey of care to have access of information of what they've been through and I am desperately sorry that occurred."
O'Neill said her decision to resign was not directly related to the abuse in care inquiry, but it had been big few years leading her organisation through its response to it.
"It does take a toll, it is something that sits with you, it doesn't leave you.
"That's been a great deal of work to produce, collecting all the information together, carrying out an investigation, dealing with anything that we've had to and walking alongside survivors is a massive piece of work and everybody here has done a phenomenal job ... and so after five years and all of the dealings like Covid etc, I think it's now time for somebody else to take the reins and lead the organisation forward from here."
O'Neill's last day at PSO will be 9 August, and Robbie Moginie has been appointed as the acting chief executive, commencing 12 August.
New Zealand Law Society president Frazer Barton is taking a leave of absence, following a complaint about the legal advice he provided before PSO destroyed records of children in its care.
The complaint was lodged by Sam Benton, who is a partner at Cooper Legal - a law firm representing survivors of abuse in care since the 1990s.
According to the commission's report, when Barton was asked whether the records could be destroyed, Barton said they could, at an "appropriate milestone or anniversary".
Barton told RNZ he did not know that in 2017 and 2018 there was the possibility of an inquiry into abuse in care and that the records would have been crucial for that reason.
"My advice to destroy them at an appropriate time, that's not go ahead and destroy them now," he said.
Barton is a partner at the law firm Anderson Lloyd.
Anderson Lloyd said the issue concerning the destruction of documents by PSO was now the subject of Law Society complaints and they supported that process.
"The Abuse in Care Royal Commission report was heart-rending, and our sympathies lie with the abuse survivors," the firm said.
"Frazer remains a partner at Anderson Lloyd. He is a highly respected senior lawyer and is a close colleague and friend to many in the firm. This is a difficult period for him and his family, after many years with Anderson Lloyd and service to the wider community, and we are supporting him."