The event held at Tūhura Otago Museum was one of only two in-person apologies organised around the country — the other to be held in Auckland next Saturday.
About 50 people were in attendance.
Presbyterian Church of Aotearoa New Zealand (PCANZ) moderator Right Rev Rose Luxford extended the "sincere and unreserved apology" on behalf of the church — past and present —to those the church and the people in it had harmed, abused, neglected and caused pain.
"It was our responsibility to care for you.
"We failed."
The abuse occurred in places and with people where safety should have been assured, Right Rev Luxford said.
"Such a breach of trust is unjustifiable.
"We express profound remorse at this heartbreaking abuse.
"We are deeply and sincerely sorry."
The church announced it would deliver a public apology in October last year.
That was in response to the findings contained in the Royal Commission of Inquiry into Abuse in Care’s 3000-page final report, released about three months earlier.
The church in a statement acknowledged its previous redress attempts were inadequate "and, in many cases, retraumatising for survivors".
"Responses were inconsistent and often delayed, while legal strategies placed the protection of the church ahead of the needs of survivors."
It had since commissioned an independent auditor, who would have full access to church policies, frameworks and records to analyse where changes must be made.
The apology was developed in part by the church’s new survivor advisory group and acknowledged "decades of physical, sexual, emotional, psychological, cultural, and spiritual abuse across Presbyterian churches", it said.

"They tried to break us, one by one.
"But together, now, we are unbreakable"
Mrs Tagaloa, who is also a member of the church’s survivor advisory group, called the abuse in care "a national tragedy" and "our country’s shame".
She noted the government was still yet to deliver on its promise to have a new single redress system up and running this year.
When coming forward, survivors had, instead of care, received "cold, clinical letters crafted by lawyers about minimising liability and protecting reputation".
Mrs Tagaloa said while she may trust the church’s intentions, many survivors would find it hard to trust the apology.
"And if you're expecting forgiveness, you need to understand that forgiveness has to be earned.
"Some survivors will never forgive — and that's their right."
She called on the church to be a champion for all survivors.
"We will watch, and we will see what you do, and we will hold you to account."
Right Rev Luxford said many survivors who had disclosed abuse to the church were met with "denial and silencing".
"We recognise the cruelty that has also led to intergenerational trauma and its lasting effects on you, your whānau, and your wider communities.
"We apologise sincerely for this immense burden."
The church also announced a new holistic redress system to replace its previous approach.
It included wellbeing support coordinators acting as first points of contact for survivors, independent navigators to help survivors through the process and provide them with redress options — such as financial compensation and personal apologies — and a panel of independent investigators to investigate reports of abuse.