Cardinal John Dew made the apology at the Royal Commission into Abuse in Care on behalf of the bishops and congregational leaders in New Zealand.
He said the church can offer no excuses for the actions of the church that caused harm.
Cardinal Dew said the abuse was perpetrated by people, such as priests, brothers and sisters and lay people that victims should have been able to trust.
He acknowledged the abuse caused pain, hurt and trauma which continues to have an impact on the lives of survivors.
Cardinal Dew described the abuse as unacceptable and indefensible and said the church was deeply sorry.
He said the systems and culture of the church allowed abuse to occur.
''These systems and culture failed you and must change."
''We apologise for the time we or our predecessors protected the church and not you.''
He said the church failed to listen to survivors, learn form them and refused to hear what they were saying.
''We acknowledge this compounded the hurt and suffering and acknowledge the ongoing physical, emotional or spiritual trauma you experienced.
''We apologise for our inappropriate responses for all we could have done but failed to do and for the times you were dismissed, ignored, not believed, belittled, forgotten.''
He said church leaders were committed to ensuring a safe church.
''Committed to putting you victims and survivors of abuse and your whānau first.''
Dew said the church remained committed to listening to victims. It would learn from what it heard, act on it and do all it could to address the harm done to them, he said.
