It could hardly have been a more public reprimand to a man who has openly championed the need for accountability in the Irish Catholic church. But Archbishop Diarmuid Martin's chosen method for delivering the Pope's message last week was notably low key.

Far from launching a verbal "hand grenade" during a speech at a high profile gathering of the faithful, for example, he quietly buried the news in a longer three-page letter which concerned itself mainly with the logistics of administering the sacraments of baptism and confirmation.

"Following presentation of their resignations to Pope Benedict, it has been decided that Bishop Eamonn Walsh and Bishop Raymond Field will remain as auxiliary bishops and are to be assigned revised responsibilities within the diocese. This means that they will be available to administer confirmation in any part of the diocese in the coming year," he wrote in the letter sent to priests in his archdiocese.

Some of his fellow bishops also privately confided last week that the first they heard of the Pope's decision was when they turned on the radio to hear the news headlines.

Be that as it may, Martin is nobody's fool.

He will have been only too aware that once the contents of the above paragraph from the letter became known, regardless of the context in which it was delivered, its impact would be immediate.

Challenge to authority

Pope Benedict's decision not to accept the resignations of two men who report directly to Martin represents arguably the most serious challenge to his authority since he succeeded Cardinal Desmond Connell as archbishop in April 2004.

This is in no small part due to the fact that both men only offered their resignations to Rome after Martin repeatedly called on all of those bishops named in the report of the Murphy commission to explain themselves.

Ultimately, the pressure he applied led Bishops Walsh and Field to make their dramatic announcement that they were resigning last Christmas Eve.

The fact that neither were heavily criticised in Judge Yvonne Murphy's report has prompted some to suggest that the Vatican deemed the report's conclusions insufficient grounds for resignation, amid concerns of a potential "domino effect" which such a precedent would set.

This is particularly true if, as seems highly likely, it is to emerge that other Irish bishops have also mishandled allegations of abuse, although it does not explain why the resignation of another bishop who featured in the report, Jim Moriarty, was accepted by the Pope last April.

Vatican observers have pointed to the fact that the decision not to accept the original resignations is highly unusual. As a result, others believe it can only be explained by the fact that there was communication between the two bishops and the Holy See since they announced their decision.

The Vatican correspondent with the Milan daily newspaper Il Giornale, Andrea Tornelli, even suggested last week that the two auxiliaries had sent a dossier to the Congregation of Bishops prompting the Vatican to reconsider their resignations.

Writing in his blog, Tornelli said Bishops Walsh and Field had made it clear to the Holy See that, while they had offered to resign in a spirit of healing and reconciliation, they themselves felt that they had done nothing wrong. Although falling short of a full withdrawal by the two men of their resignations, such actions may well have been seen by the Pope's advisers as a good reason to reject them.

In the absence of any sign that Rome will explain the decision publicly – Vatican spokesman Fr Federico Lombardi has said it is not "policy" to comment on resignations which had not been accepted – the decision raises a number of troubling questions for Martin.

The harsh reality is that he now faces the prospect of working on a daily basis with two men whose removal from office he championed, however indirectly.

They meanwhile have the imprimatur of a higher authority – and in the Catholic church there is no greater power than the Pope himself – and could be forgiven if they become emboldened in their dealings with their superior.

It remains to be seen how Dublin parents will react when both men start to resume their participation in confirmation ceremonies next year. But in a high stakes game of clerical poker, they have come away with a "trump card".

Not surprised

Prominent clerical abuse survivor and campaigner Marie Collins watched last week's events with mixed emotions. In one sense she was "not surprised at all" that the resignations were not accepted, given the length of time the Vatican has taken to make its decision known. Yet she has been left distraught at what it means for the Catholic Church to which she belongs.

"It is the final nail in the coffin of any hope I had left that the Catholic Church was going to change, or that it had any intention of listening to the laity. It is still a clerical church," she says. "I think the worst aspect of the whole thing is that Diarmuid Martin's authority has been undermined ... I think he acted correctly in encouraging the resignations of the two auxiliaries not for what they did, but what they did not do. They weren't powerless.

"If Bishop Moriarty [whose resignation was accepted by Pope Benedict] knew about abuse as an auxiliary, then they did too. They could have gone public, I know it would have been detrimental to their careers but it would have saved more children from abuse."

Among the few options open to Martin now, she believes, is to simply keep his head down, stay quiet and accept the slap on the wrist from the Vatican that he has received.

"Or he can simply speak out and express whatever feelings he has. But I don't know whether he would be willing to do this; there is now a huge warning there not to go against the status quo as Diarmuid Martin did," she says. "The ground has been taken out from under him. He can either just take it and carry on, which is what the Vatican would expect, I suppose. Or he can speak out and resign."

On a more personal level, last week's events have prompted Collins, who has previously described herself as someone who was clinging onto her faith "by her fingernails", to seriously question for the first time whether she can continue in the Catholic Church.

"We had the letter from the Pope in March, and we were disappointed with that. It had a lot of fine words, but the actions are not living up to those words. And yet you still hang on there, hoping it's going to change. And we had the bishops offer their resignations. Only one of them [Moriarty] was apparently sincere and acknowledged it was because he didn't challenge the culture of the church at the time," she explains.

"It would appear that these two others were not sincere, and still believe they did nothing wrong. But if those two had stood up, children would have been stopped from being abused. The fact that the Pope doesn't see that is the final straw for me."

"I have always said my Christianity is not in doubt. I am not disillusioned with my faith in God or Christ. But I am just at the point where I'm considering that I don't need to call myself a Catholic any more, in a church where clerical power holds sway. My hope of reform coming from within the clerical church is gone."

The fact that the Pope now appears to be differentiating between acts of commission and acts of omission is another deeply worrying development for her too.

"Children continue to be abused in both cases; it allows the abuse to continue. If you stand by doing nothing it has the same effect," she says.

"I would be considering leaving at this point. When I was clinging on to my Catholic faith with my fingertips in the past, I still had hope. And Diarmuid Martin was a symbol of that. I would definitely see this as the end of any hope that things are going to change. So I'm at the point definitely of thinking this is not the Church for me. I'm not just saying that for effect. I just can't see any glimmer of hope, any reason to stay. I'm totally shattered at this point."

Falling into line

For all his outspokenness on issues relating to clerical sexual abuse, Diarmuid Martin has pointedly confined himself to criticising his fellow bishops and priests in Ireland. You do not become an archbishop by being a vocal critic of the Vatican or its teachings.

Martin is also a career Vatican diplomat, well versed in how to operate within its intricate power structures, rather than openly questioning its decisions.

So the fact that he did not respond to queries from this newspaper last week – he is understood to be on annual leave in Italy – indicates that he has little intention of breaking rank.

Some also believe that despite how it may appear, it is highly unlikely that the decision to reject the resignations of Walsh and Field would have been made without his agreement. As a result, they say this is no longer a resigning matter, if it ever really was.

Michael Kelly, deputy editor of the Irish Catholic, which was first to publish details of the leaked letter from Martin last week, says he would probably have known about the Pope's decision for at least two weeks, as the entire Vatican closes for business during the month of August. Others suggest he may have known since as far back as March.

Kelly says the decision confirms the suspicions which some, such as abuse survivors, have that Martin effectively had his "wings clipped" during last February's meeting of the Irish bishops with the Pope in Rome.

It might also help to explain what some believe have been his increasingly "tetchy" public statements in the intervening months.

"The Archbishop was not neutral in all this. He wanted them to resign, he was very clear on that," Kelly says. "So they've won, if you like. The Vatican has backed the auxiliaries rather than their archbishop. it believes there has been an injustice done against them.

"So to some extent they have been rehabilitated, and whether Diarmuid Martin has confidence in them is no longer really relevant. The people above him in the Vatican do."

Kelly believes the Vatican is generally happy with the line Martin has taken in confronting clerical sexual abuse in his archdiocese, but is anxious to avoid any public disputes among fellow bishops.

"This decision would not have been foisted upon Martin. He may have been reluctantly convinced to accept it, but if he had been dead set against it, I don't think it would have happened. They would have been worried about forcing him to resign, so in some way, he has reluctantly agreed to a compromise," he adds.

This raises an­other intriguing possibility. Martin has long been rumoured to be on the verge of re­turning to his previous stellar career in the Vatican. If he believes he will not be in his post for much longer, then the "indignity" of having to work on a daily basis with Bishops Walsh and Field may be a relatively temporary inconvenience perhaps secured with the promise of a plum Vatican posting as a reward for obedience in the short to medium term.

As the Pope prepares to send a hardline apostolic delegation here to commence his much publicised "visitation" of the Irish Catholic church, this begs the further question: has the search for a potential successor to Diarmuid Martin begun?