It says most abuse survivors surveyed were not satisfied with the outcomes when they engaged with the Church.
One recommendation is for two new independent charities funded by the Church to take over the protection of children and vulnerable adults.
The report will be discussed at the General Synod this weekend.
It was written by Professor Alexis Jay, the former head of the independent inquiry into child sexual abuse.
The archbishops of Canterbury and York welcomed the report's "wisdom, expertise and meticulous proposals."
Professor Jay, one of the most experienced and respected voices on safeguarding issues, has laid out bold and clear recommendations that leave little room for misunderstanding.
"Further tinkering with existing structures would not be sufficient to make safeguarding in the Church professional, accountable and trusted by those who use its services," she says.
"The only way in which all of these concerns could be addressed is through the establishment of two separate charities, independent of the Church, one with operational responsibility for safeguarding and the other to provide scrutiny. "
She says the proposed new independent bodies need to be funded by the Church and that anyone complaining of abuse in the Church should be referred to them as soon as possible.
The first organisation would conduct investigations and support victims and survivors. It would also provide safeguarding training.
The need for a second charity to monitor and evaluate the effectiveness of the first is because the Church has not been able to do a good job evaluating its own progress until now.
"There are conflicts of interest in several aspects of safeguarding, which are not openly acknowledged or addressed in policy, procedures or practice. This serves to further undermine the trust of many of those who need to engage with Church safeguarding," Professor Jay says in one of her conclusions.
She recognises the good work being done by individuals in churches, but her report talks of huge inconsistencies in the way abuse allegations are dealt with across the Church of England's 42 dioceses.
"It is important to say that the criticisms set out in the report are not a reflection on individual safeguarding professionals, but rather of current structures and processes which need to change. It is now the task of the Church of England to take the report's recommendations forward," she says.
Professor Jay was called on for advice by Church leadership last summer at a time of crisis.
Then, the Church's Independent Safeguarding Board had just been dramatically disbanded. Panel members accused the Church of being obstructive in their work, and the relationship between the Church of England and survivors of abuse appeared to be as strained as ever.
This sentiment was reflected in Professor Jay's research which included a survey of people who had interacted with Church safeguarding systems in the past five years.
Some survivors even talked of feeling like the system had, in their words, been "weaponised against them" and many respondents (which included clergy and church volunteers) reporting an "all-time low" in relations between Church and survivors.
In spite of numerous reviews and the Independent Inquiry into Child Sexual Abuse chaired by Professor Jay, the Church has yet to prove it is able to keep people safe without outside involvement.
"We thank Professor Jay and her team for this fully independent report, and the wisdom, expertise and meticulous proposals contained within it," the Archbishop of Canterbury, Justin Welby and the Archbishop of York, Stephen Cottrell, said in a statement.
"We recognise her criticism of our safeguarding structures and processes and we welcome this scrutiny and challenge. For the sake of all those who come into contact with the Church, particularly victims and survivors, we welcome the plans that are in place to take forward this work as swiftly as possible."