Her resignation comes after it was revealed that 206 women were wrongly diagnosed following routine smear tests.
The clinical director of the CervicalCheck programme, Dr Grainne Flannelly, has stood down from her role "with immediate effect".
They say any woman who may have not been told that her case has been audited has been informed - or will be informed after the weekend.
Responding to the controversy, the Irish Cancer Society extended its sincerest sympathies to Ms Phelan and her family.
In relation to queries from RTÉ News, as to whether there are any other cases of missed cervical cancer diagnoses, the HSE said it was not possible to get this information at this time of the evening.
Ms Phelan, of Carrigeen, Annacotty, Co Limerick alongside her better half Jim Phelan has sued the Health Service Executive and Clinical Pathology Laboratories Inc, Austin, Texas, over a spread test taken under the National Cervical Screening Program CervicalCheck and dissected in the United States research facility.
"[My doctor] told me he knew of three", she says. I have made a decision to step aside to allow the Programme to continue it's important work.
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"The HSE has confidence that the programme's leadership team is dedicated to this important goal and is working hard to meet it".
A 43-year-old woman who was given mistaken test outcomes and is now critically ill with cervical cancer has settled her High Court activity against a USA lab for €2.5m.
It is amid revelations that more than 200 reviews of tests suggested women with cervical cancer should have received "earlier intervention".
She was only informed of the misread test past year, and her case only came to light in an audit after she had been diagnosed with cervical cancer in 2014.
The court was told that CervicalCheck informed Ms Phelan's consultant about the mistake in 2016 but there was a further delay until 2017 before she was told.
Professor Shepherd said in his opinion this delay was "most irregular" and absolutely should not happen.
"I am terminally-ill and there is no cure for my cancer".