The Most Rev Justin Welby told the hearing that the last three weeks of evidence relating to child sexual abuse in the Church has horrified him.
Asked what he had learned from the hearings, Mr Welby paused and appeared to be fighting tears as he said: "I have learned to be ashamed again, in the past three weeks.
"You can't read the transcripts, you can't read the evidence statements, without being moved - at least you shouldn't be able to.
"And the Church does wonderful wonderful things, you know, across the country, extraordinary things.
"The most stressful job in the Church is to be a parish priest, and to be a good parish priest.
"And that a small minority have betrayed that is horrifying.
"I don't think I was ever complacent at any point. I hate this too much to be complacent."
He added: "I want to put on record again - I don't know how to express it adequately - how appalled I am and how ashamed I am of the Church for what it did to those who are survivors and are coping with this.
"The apologies are fine, but you have got to find ways of making it different and we have got to do it as soon as possible."
Earlier, the Archbishop said that meeting victims reading their statements had been "horrifying".
He told the Independent Inquiry into Child Sexual Abuse that while the perpetrators may be forgiven, they could never be trusted again.
Giving evidence at the inquiry on Wednesday, he said: "The Bible is utterly brutally blunt about the difference between forgiveness and the consequences of sin.
Mr Welby said: "Where there is something done wrong, there will be consequences.
"If someone has been an abuser, they can never be trusted again, that is the consequence."
Fiona Scolding QC, the lead lawyer for the Anglican strand of the inquiry, asked the Archbishop how the Church is addressing the issue of safeguarding.
He replied that he had implemented training, but that there was also a great need for a culture change.
On the blame culture in the Church, Mr Welby said: "'I've heard about a problem, but it was someone else's job to report it'.
"That is not an acceptable human response let alone a leadership response. If you know a child is being abused, not to report it is simply wrong."
Mr Welby also told the inquiry that it was taking too long for abuse victims to get justice.
He said: "We end up hurting people more because it doesn't seem to follow.
"People are not informed, they are not told what is going on.
"It can take three or four years and you end up damaging the survivors and victims more. You abuse them in the way you keep them waiting, and for that matter you don't do justice to the perpetrator.
"And at the heart of this has to be justice, and justice is very very difficult to find.
"But you have to have a system that delivers justice. That is so important and if it doesn't, it is not good enough and therefore if you can't do it through the present system then you have to find another that will be more reliable."
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