The speedy departure of the leading advocate of bringing victims into fuller dialogue with the church authorities sparked off a wave of speculation that he was isolated from the other bishops.
Dr Martin had promised victims of clerical abuse in his Dublin archdiocese to make known to the pontiff their demands that Bishop of Galway Martin Drennan should resign or be removed from office.
He had also promised survivors of institutional abuse by religious orders in industrial schools to bring to the Pope their request for a meeting with the him at the Vatican.
Neither of these two demands were addressed in the statement issued by the Vatican in which Pope Benedict claimed that a weakening of the Catholic faith in Ireland had been "a significant contributing factor in the phenomenon of the sexual abuse of minors".
Pope Benedict also expressed his hope that his participation in the two-day talks "would help to unify the bishops and enable them to speak with one voice", a statement that sounded like a rebuke to Dr Martin for his public call on Bishop Drennan and the other auxiliary bishops of Dublin to be accountable for their part in a culture of cover-ups condemned by the Murphy report.
The Pope instructed the bishops to speak with one voice "in identifying concrete steps aimed at bringing healing to those who had been abused, encouraging a renewal of faith in Christ and restoring the church's spiritual and moral credibility".
These comments, released by the Vatican press office, instantly enraged victims in Ireland who saw it as a charade and an insult.
Asked by the Irish Independent about the disunity among the bishops over the "divisive" continuation in office of Bishop Drennan and the failure of the Pope to invite victims to Rome, Cardinal Brady said: "I want to make it quite clear that there is no disunity among the Irish bishops concerning the importance of the safeguarding of children.
"We have all signed up to the national guidance material which we have prepared with the National Board for the Safeguarding of Children and we are implementing it. So there is no disunity in that regard."
The cardinal was also asked if Dr Martin's decision to return from Rome to attend an Ash Wednesday public engagement at UCD was because of tensions among the bishops.
The cardinal replied: "Archbishop Martin's absence is most certainly not -- most certainly not -- due to tensions among the bishops.
"During the five days we spent last week in Knock, and these two days in Rome, our unity has never been greater," added the cardinal, claiming that the talks with the Pope and senior cardinals of the Roman Curia had amounted to "a mini-Synod".
"Each of the 24 bishops spoke for five minutes from their hearts and their heads with passion on these (abuse) issues which have engaged so much of our time, energy and resources," he added.