Vicky Phelan's botched smear test uncovered a scandal within CervicalCheck.
The investigation will place a particular focus on the quality assurance systems, clinical audit processes and the communications with patients, according to the minister.
Simon Harris, the health minister, said that the families of all those who died would be informed about the audit by today.
Taoiseach Leo Varadkar confirmed today that the Government will hold an inquiry into the failure of State's national cervical cancer screening programme to tell women they were falsely given all-clear smear tests.
Under the auspices of this investigation an worldwide peer group will also be established to review root and branch our cervical screening programme in Ireland against best global standards and practices.
Reacting to the news that there is to be an inquiry into the scandal, Ms Phelan said: "What I don't want to see is - the minute I heard that announcement this morning it raised waning signals with me - what I don't want to see is an inquiry or tribunal that's going to take years and is going to be dragged out".
The HSE says it can not confirm reports that 12 women whose cancer diagnosis was delayed have died.
175 out of 208 women with cancer would have benefited from earlier treatment, while 162 that were part of a look-back were not told about the review or its outcome.
Legislation is also due to be brought forward which would make it mandatory for doctors and medical professionals to engage in "open disclosure" - ensuring patients are notified of serious events relating to their care.
"I don't think anyone could have imagined the magnitude of this".
'In addition I am appointing an International Clinical Expert Panel to provide the women concerned with an individual clinical review.
Mr Lynch also noted that the number of women affected by this controversy is 208, not 206. Thankfully I didn't and I'm here to tell the tale.
The number is 1800 45 45 55.