Update 7.10pm: Dr Gabriel Scally has said that completing the report into CervicalCheck is "much more complex than we could have imagined at the beginning".
Dr Scally was due to complete his scoping inquiry this month but now says it will take until the end of the summer.
Speaking to RTÉ Radio 1 Drivetime, Dr Scally said that he had not expected the difficulty he has run into in obtaining the necessary information.
He denied reports that the delay was caused by his interaction with the women involved saying that they have been "absolutely fantastic".
"The problem is the volume of information that we're going to have to go through and its availability to us, because it is not yet coming either in quantity I would want it or in the way I would want it," Dr Scally explained.
"It is unacceptable to be given reports that were generated relatively recently in a modern format for us to be sent them in a photocopied format that we can't search.
"When we are dealing with thousands and thousands of files it is really important that we are able to do a decent job searching through those."
Despite difficulties, Dr Scally does not believe that he is being stonewalled.
Still having discussions with the HSE, he says that things are slow.
Let me be crystal clear whatever information Dr Scally requires, he must be provided with. I made that absolutely clear when I met him yesterday. I am grateful to him for his excellent work, his engagement with the women impacted & 6 key recommendations which I accepted in full— Simon Harris TD (@SimonHarrisTD) June 12, 2018
He told Mary Wilson that he will be getting in touch with Minister Simon Harris in the next day to inform him that he is not getting the information he wants if he does not get it.
"Let me make it quite clear, I will not be letting walls get in my way, whether they are stone or otherwise. I will get to the bottom of this," Dr Scally said.
"At the heart of this are a group of women who developed cervical cancer and information was known about their slides previously, they had been looked at again and in very many cases the results of those slides were changed and they weren't told."
Dr Scally is hoping to speak to as many women and families that have been affected by the CervicalCheck scandal but says that he understands that there are those who will not wish to be involved.
He will be holding a number of meetings around the country to which all of those affected will be invited and will have the opportunity to tell their stories.
On consent forms between patient and CervicalCheck screening, Dr. Scally said that he hopes to see two new statements, one being that women will have full and open access to their screening records and two, if there is a problem that it will be disclosed in a timely, considerate and accurate manner
Meanwhile, Taoiseach Leo Varadkar has defended the delay in the final report of the scoping inquiry.
"It isn't as straight forward as going to the medical records of a hospital and requesting a patient chart, medical records are about a lot more than that," said Mr Varadkar.
"They can be in a number of different places, they can be in paper format and electronic format and it doesn't just include the patient's charts in electronic records, it also includes things like x-rays, things like slides, things that may be in laboratories elsewhere."
Mr Damien McCallion, HSE National Director, National Screening Service welcomed the publication of the Progress Report by Dr Gabriel Scally today.
"The HSE is committed to learning from the failings identified in this audit and to rebuilding trust and confidence in the cervical screening programme," said Mr McCallion.
"The review team has recommended some immediate practical improvements that can be made to our cervical screening communications and health education materials.
"We are working on a project to comprehensively review the information and materials used as part of the CervicalCheck programme.
"This process will now be specifically informed by the recommendations as outlined today by Dr Scally in his progress report, and we will ensure that these recommendations are followed up swiftly within the cervical screening programme."
The HSE has said that it will continue to co-operate fully with the Scoping Inquiry, the International Expert Panel Review and any subsequent inquiries.
You can listen to Dr Scally's full interview below:
Earlier: Head of CervicalCheck inquiry critical of delay in receiving information
The head of the investigation into CervicalCheck has criticised state agencies for not getting information to him fast enough.
Dr Gabriel Scally was due to complete his scoping inquiry this month but now says it will take until the end of the summer.
Dr Scally gave a progress report to the government this morning.
He says a large portion of the 4,000 documents he has been given only arrived from the HSE, Department of Health and others in recent days and many are in formats that cannot be searched digitally.
People Before Profit TD Brid Smith says the delay is not acceptable.
Minister says delays with Scally report, HSE delays releasing women's medical reports; Govt delays releasing the stats on performance of the privatised labs this scandal starts and ends with outsourcing, no delay will hide this fact .#standing4women #CervicalCancer @Dyaneconnor— Brid Smith TD (@bridsmithTD) June 12, 2018
The Taoiseach acknowledged there has been a delay in getting documents.
But Health Minister Simon Harris defended the progress made.
Earlier: CervicalCheck inquiry to miss deadline
An inquiry into the CervicalCheck scandal is set to miss its end of June deadline.
Dr Gabriel Scally, who was appointed to lead the preliminary inquiry, was due to recommend if a commission of investigation is necessary by the end of the month.
According to the Irish Times, Dr Scally has still not spoken to the majority of people involved and is now looking at how he can get in contact with all of the 209 people affected.
Department of Health officials met yesterday with the chairman of the scoping investigation, whose progress report will be considered at Cabinet today.