Health Minister Simon Harris says he "respects" the decision of Dr Peter Boylan to resign from the board of the National Maternity Hospital.
The former Master resigned earlier from the Executive Committee of the hospital, confirming to the Pat Kenny Show this will take place with immediate effect.
In a statement obtained by Newstalk, Dr Boylan said: "I can no longer remain a member of a board which is so blind to the consequences of its decision to transfer sole ownership of the hospital to the Religious Sisters of Charity, and so deaf to the disquiet of the public it serves".
"Hospitals on land owned by the Catholic Church are obliged to follow Catholic teaching and Canon Law on medical practices and procedures.
"The proposed hospital will be built on land owned by the Religious Sisters of Charity, the hospital will be owned outright by the Religious Sisters of Charity, and the company tasked with running the hospital will be owned outright by the Religious Sisters of Charity.
"To believe the new National Maternity Hospital will be the only hospital in the world owned by a Catholic congregation to permit serialisation, IVF, abortion, gender reassignment surgery and any other procedures prohibited by the Church is naive and delusional".
The board of Holles Street voted to press ahead with building the new National Maternity Hospital at the St Vincent's campus in Dublin on Wednesday night.
It reaffirmed its commitment to the original deal by a large majority.
In a statement, the board said: "This agreement provides that the clinical, financial and operational independence of the National Maternity Hospital at Elm Park DAC shall be enshrined in its memorandum and articles of association and all related legal agreements."
Dr Boylan agreed with Pat Kenny that he he was a lone voice "more or less" at the meeting of the board.
But he said he was "not a lone voice in the community outside, to which we have a great responsibility and (to) the women in particular.
"I'm also not a lone voice among the the medical profession in that the previous Master of the Coombe Hospital, Dr Chris Fitzpatrick, and the previous Master of the Rotunda Sam Coulter-Smith have both voiced serious reservations about the governance and proposed structures".
Hear his full interview with Pat Kenny below:
In response to the resignation, Health Minister Simon Harris said: "Dr Boylan is a very respected doctor, has made a huge contribution and will continue to - I'm sure - to the healthcare of women in this country.
"He's made his decision, I respect that decision - but I also note the overwhelming decision of the board".
Dr Peter Boylan's resignation letter in full:
Dr Boylan was asked to step down after he criticised the plan to build the new facility at a site owned by the Sisters of Charity at St Vincent's Hospital in Dublin.
Concerns were raised about the potential for religious influence over the new hospital, and last week Dr Boylan spoke out about his reservations.
He said the 100 governors of the National Maternity Hospital (NMH) in Holles Street had yet to be asked for their agreement on the arrangement and insisted he had expressed his reservations to his fellow board members on a number of occasions.
Dr Boylan said yesterday the Department of Health had been warned "some time ago" that there would be ethical and ethos issues if the hospital was located on land owned by the religious group.
He said the chairman of the Ireland East Hospital group wrote to the department outlining concerns with the plan months ago - but nothing was done.
The former master of Holles Street said it is "highly likely" that the ownership issue would interfere with the new facilities ethical governance, adding that it was "a bit naive to expect that this would wash in the public mind."