He said from his review of the records of this case, Ms Phelan's test was "one of a number of smears that had been reviewed and found to be wanting".
She was diagnosed with cervical cancer around the same time but she only found out about that review past year.
Minister Harris and the HSE director general, Tony O'Brien, have agreed that an global peer review of CervicalCheck needs to take place to ensure ongoing confidence in it.
According to the HSE, nearly 1,500 cases of cervical cancer have been notified to the cervical screening programme, CervicalCheck, since it began a decade ago.
Phelan, who is a 43 year old Mother of two, was awarded €2.5 million over a missed abnormality in a smear test in 2011.
She revealed that Simon Harris had called her personally to apologise for the health service letting her down.
Asked if in his view this was appropriate to ignore her, he replied: "No, absolutely not, nor the other ten that I have referred to".More news: Steelers select WR, QB, OT in rounds 2-3 of draft
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The 206 women whose smear tests were misread should have been referred on for further investigation, including an invasive diagnostic procedure or repeat smear, which could have picked up their cancer and led to earlier treatment.
This morning, Mr. J Kevin Cross was told the case against the lab had been settled for €2.5m with no admission of liability and the case against the HSE could be struck out.
It follows the recent controversy over smear test results.
Detecting and removing abnormal cervical cells can prevent cervical cancer.
Mr Justice Cross said he was charmed that the case had settled and said to Ms Phelan: "In the event that anybody can beat this, you can".
"As soon as I heard the voice I knew who it was and he said "hi Vicky, it is Simon Harris here", Ms Phelan explained.
The HSE said it wished to acknowledge Professor Flannelly and to formally thank her for "the enormous dedication, contribution and expert knowledge" that she brought to the CervicalCheck Programme over the past 12 years.
"It has helped reduce the cervical cancer rate nationally at a rate of 7% per year".