According to a story told by Dr Peter Boylan, he and Dr Rhona Mahony were not always so divided on the future of the National Maternity Hospital. Dr Boylan, a former master of the hospital, and Dr Mahony, the current Master who also happens to be his sister-in-law, had offices beside each other in the crumbling Holles Street building.

Dr Boylan claims that in May last year, Dr Mahony asked him to write to the Minister for Health and to the board of St Vincent's Healthcare Group "expressing concerns about the nuns' potential involvement" in the National Maternity Hospital. He says he was asked to write because he was chairman of the Institute of Obstetricians and Gynaecologists.

Dr Boylan says he duly wrote the letters. But since the agreement was drawn up last November, he and Dr Mahony are no longer on the same side of the fence. "It would appear her concerns have been allayed by the proposed agreement. Mine have not obviously," says Dr Boylan.

Dr Mahony denies this ever happened. In a statement to the Sunday Independent, she says she did not ask him to "write to St Vincent's Hospital or the minister in relation to nuns. The correspondence referenced and other public statements made by the institute at that time were not made on behalf of the hospital and this was made clear publicly at the time". The statement says she had asked him in his role as chairman of the institute to give his opinion on governance structure being proposed by St Vincent's, and that was in March last year.

Dr Boylan is in the sunny, book-lined kitchen of his south Dublin home. Harry, the Irish terrier, bounds in after his morning walk with Jane, who is Rhona's sister.

He insists that his personal and family life is strictly out of bounds. He is friendly and speaks with calm and level delivery, which probably belies the personal toll of this row. He says he never wanted it to become personal, but personal it has become.

He is at the end of a two-week storm which began with him giving a radio interview expressing his fears about religious interference if the Sisters of Charity are given ownership of the maternity hospital.

Dr Mahony and Nicky Kearns, the National Maternity Hospital's deputy chairman, shot back, accusing Dr Boylan of spreading inaccuracies and misinformation, and stressing the urgent need for a new building.

Things came to a head last Sunday when Dr Boylan texted Dr Mahony and Kearns, claiming they had been misled by St Vincent's. Kearns texted back, asking him to resign. He did after last Wednesday's board meeting when the executive directors overwhelmingly endorsed the terms of agreement - including the obstetricians. Dr Boylan, a Sinn Fein councillor and a Labour Lord Mayor were the only three against. The day after the vote, Dr Boylan resigned.

"What's in it for me is pressure, stress. You know, the easiest thing would be to say nothing, to go home. It is interfering in my life in a major way. So there is nothing in it for me. This is for women," he says.

"I spent my entire career trying to make things better for women's healthcare. To have spent my entire professional life in Holles Street and then to see it given over to the Sisters of Charity just breaks my heart. These are important issues. What has helped me is the overwhelming support from right around the country and abroad. It's just overwhelming."

Shortly after he became master of Holles Street in 1991, Dr Boylan was once summoned by Desmond Connell, the late Archbishop, and ordered to stop performing tubal ligations.

"I went up with the matron at the time. We got out of the car and we were shown into a room with Archbishop Connell and I think it was Bishop Moriarty sitting across the table from us. He said: 'You can't do tubal ligations.' I said: 'We can'."

He recalls Archbishop Connoll then said: "Well, you're to stop" - to which he replied: "Well, we're not."

Few obstetrician would disagree with Dr Boylan's view that healthcare should be provided without religious restriction. Where he and Dr Mahony vehemently differ is in whether the terms of agreement that will underpin the relocated hospital in St Vincent's will ensure religious influence is kept at bay. The terms of agreement - revealed first by the Sunday Independent last weekend - were hotly debated last week.

Under its terms, St Vincent's will have 100pc ownership of the new National Maternity Hospital at Elm Park. Decisions affecting the hospital's clinical independence can only be altered with a unanimous decision by the board of directors, plus the agreement of the health minister.

The nuns will own the building and the company but it can only be used as a maternity hospital - they can never sell it or use it as collateral against a loan because the State will have a lien on it. Dr Boylan has gone through it line by line and taken issue with most of it. The question he keeps asking is why do the nuns want to own a hospital that would be required to perform procedures that are at odds with their Catholic ethos?

One source close to the talks insists St Vincent's requires ownership for the smooth operation of the vast campus at Elm Park - it fears having a separate legal entity on its own grounds could have serious implications for the campus's future development, by objecting to planning applications, for instance.

Dr Boylan claims St Vincent's is interested in the €300m it will get on its balance sheet. He claims there's no reason why the footprint of the hospital could not be transferred into the ownership of the State. As it is, St Vincent's doesn't own the Breast Check building on its grounds.

Sources close to the negotiations say that the National Maternity Hospital did raise this in negotiations. St Vincent's insisted that it was a small, peripheral building on the boundary of the campus that didn't really impact on its activities. The National Maternity Hospital, on the other hand, would be right at the heart of its campus.

Dr Boylan claims the board's independence is also "fragile" - a director approved by St Vincent's will effectively hold the casting vote.

Does he trust any of the provisions in the terms of agreement? He pauses for a second and laughs: "No."

With the endorsement of the board of the National Maternity Hospital and similar unanimous backing from the board of St Vincent's last week, the deal appears to be going ahead. The terms of an agreement will be worked into a legal document in the coming weeks, under the auspices of the Department of Health.

Pressure is mounting on Simon Harris - whom Dr Boylan claims sided with St Vincent's in the talks, enabling it to play hardball - to revisit the issue of ownership.

Sinn Fein will be tabling a motion demanding public ownership of the hospital this week and Micheal Mac Donncha, a Sinn Fein councillor on the NMH's board who voted against the agreement last week, says: "The ball is now in Simon Harris's court."

Dr Boylan hasn't had much public support from his colleagues. Two former masters, Sam Coulter Smith of the Rotunda and Professor Chris Fitzpatrick at the Coombe, have supported him. Prof Fitzpatrick was on the development board overseeing the National Maternity Hospital move. He resigned that post last Thursday in solidarity with Dr Boylan, describing the arrangement with St Vincent's as a "forced marriage".

Dr Coulter Smith told the Sunday Independent that there is no ethical interference in the three maternity hospitals now and that must be maintained. "There is a huge swathe of opinion, a lot of people, who have difficulties with a religious order having ownership of a maternity service. In an ideal world, this would not happen," he says.

One obstetrician claims that doctors don't have a great record of challenging the status quo, particularly the HSE and the minister. Dr Boylan says he understands: "A lot of people are reluctant to put their head above the parapet because if they do, the next thing you know you have a lot of journalists ringing you."

Meanwhile, the wave of public concern continues to gather momentum.

Krysia Lynch, of the Association for the Improvement of Maternity Services Ireland, said the association has been "inundated" with calls from women looking for clarity over the role of the Sisters of Charity in the hospital.

Niall Behan, chief executive of the Irish Family Planning Association, told the Sunday Independent it was questionable for publicly funded institutions such as hospitals to have "conscientious objections" about certain services.

The Sisters of Charity could help ease concerns. The order has made no public statement, bar an ambiguous quote obtained by The Irish Times from Sister Agnes Reynolds, a 79-year-old nun who is on the board of the St Vincent's Group, who declined to say whether her order's ownership of the maternity hospital would influence medical care.

A Sisters of Charity document dated 2010, which was unearthed by one newspaper last week, makes things clear. It outlines the sisters' hospital rules: no morning-after pill, no vasectomies, no sterilisations of women; no invitro-fertilisation and a commitment that "life" is to be protected from conception onwards.

The agreement shows no signs of being thrown off course. After a brief wobble on St Vincent's part, both sides seem more united than ever in driving through the much-needed facility. The cabinet has endorsed it, despite Dr Boylan's misgivings. Lawyers are poised to begin work on turning the agreement into a legal document.

The argument is no longer just about whether the National Maternity Hospital can offer independent medical care to women on the St Vincent's campus. It is a broader one of religious influence on taxpayer-funded heath facilities. The National Maternity Hospital's plans for co-location don't have to be sacrificed to in this debate. The nuns could relinquish ownership, says Dr Boylan. "That would solve everything."