Dr Gabriel Scally has been reviewing the cases of 209 women who received false negative results from the State's national screening programme.
They were not informed when the issues were brought to light by an internal audit.
The review highlights "serious gaps" in the screening programme.
Dr Scally says: "It is apparent that there are serious gaps in the governance structures of the screening services.
"In the specific case of Cervical Check, there was a demonstrable deficit of clear
governance and reporting lines between it, the National Screening Service and the higher
management structures of the HSE.
"This confusion complicated the reporting of issues and multiplied the risks.
"It is clear that there are also serious gaps in the range of expertise of professional and managerial staff directly engaged in the operation of CervicalCheck.
"There are, in addition, substantial weaknesses, indeed absences, of proper professional advisory structures.
"These deficiencies played no little role in the serious issues that concern this
Scoping Inquiry.
He adds: "I am satisfied with the quality management processes in the current laboratory sites i.e. CWIUH, Quest, and the Sonic Healthcare Laboratories, namely MLP and TDL.
"I am also satisfied that the quality management processes were adequate in the former provider, CPL in Austin, Texas, part of Sonic Healthcare."
Overhaul
It also says that the programme should be overhauled.
The report says: "Within three months of the publication of the Scoping Inquiry report, there should be an independent review of implementation plans to be produced by each State body named in this report, in respect of the recommendations contained herein.
"The findings of this independent review of implementation plans should be submitted to the minister and published.
"Thereafter, there should be a further review of progress reported to the minister at six monthly intervals and published."
Recommendations
Dr Scally has made 50 recommendations - but has not singled out anyone for blame.
He has also concluded that the labs carrying out testing on behalf of the programme should be allowed to continue their work.
His team has interviewed all of the key stakeholders and visited the labs used by the screening programmes.
He has also scrutinised 13,000 pages of documents.
It comes after key details of Dr Scally's findings were leaked in the media on Tuesday, before those affected by the scandal could be briefed.
The Health Minister Simon Harris has not ruled out setting up a Commission of Inquiry.
He has welcomed the report and says he is committed to implementing the 50 recommendations.
Independent Patient Advisory Council
The Health Minister Simon Harris has not ruled out setting up a Commission of Inquiry.
But he has welcomed the report and says he is committed to implementing the 50 recommendations.
Speaking to Dr Ciara Kelly on Lunchtime Live, Mr Harris says: "He talks about the need to enhance the voice of the patient - so I've decided today I'm going to establish an Independent Patient Advisory Council - and I'll bring proposals on that next month".
"He talks about the need for the Medical Council to tighten up its own guidelines on open disclosure, so that doctors have absolute clarity.
"He want us to legislate for duty of candour so that it's not optional as to whether you tell the patient when something seriously goes wrong - and there are many, many other recommendation as well in relation to procurement, in relation to the governance structure of screening, having a national director of screening so there's one individual in charge of it.
"There's definitely a lack of role clarity in there."
