It comes after the Royal Commission of Inquiry into historic Abuse in Care requested Gloriavale apologise to its members, last July.
Overseeing Shepherd Howard Temple delivered an apology to the community on behalf of the church on Sunday.
He said the organisation acknowledged that abuse happened within its community between 1950 and 1999.
"To the people of Gloriavale and those who were part of the community that experienced this abuse while amongst us, we write to you with profound sorrow, acknowledging the pain and suffering that has been experienced by victims and families while within our church group."
Temple said the church offered its "deepest apologies" for the abuse and that the leadership of the time had not reported known instances of abuse to the authorities.
He said the church's members were entitled to a safe and supportive environment - which it intended to provide - but it failed to do so.
"We thank the people who have spoken up and brought this sin into the light where it could be dealt with.
"We honour your courage, and we also acknowledge those who struggle to find the words to express their pain."
He said the trust that should have been honoured within the community was broken and for that, it was deeply sorry.
He said Gloriavale would listen to victims and support them to heal and receive redress.
"As part of our commitment to change, we have provided, and will continue to provide, abuse awareness and prevention training to our children and families, promoting a culture of vigilance and care.
"We are committed to making our processes robust and consistent. We commit to the highest standards of pastoral care."
Temple said the church planned to create a page on its website where abuse could be reported and people could find support from external agencies.
Victims could request a personal apology from the leadership on behalf of the church for not reporting known case of abuse to the appropriate authorities.
To ensure the safety of its members, the church had also implemented processes to guide and support members to be safe and get help from external agencies as required.
