The Bishop of Limerick Dr Donal Murray bowed to the inevitable yesterday when he resigned over his "inexcusable" investigation into the Dublin paedophile priest Fr Thomas Naughton.

The Pope has already expressed his personal distress over the Murphy Report.

And he has promised a rare Pastoral Letter directed to the Irish people early in the new year.

The long-term challenges remain extremely serious and the dramatic meeting in Rome last Friday between Pope Benedict, the Irish Primate Cardinal Sean Brady and the Archbishop of Dublin Dr Dairmuid Martin underlined the gravity of the situation.

The scandalous revelations in the Murphy Report of attempted cover-ups of the abuse of children are indicative of a church that has failed to come to terms with the proper exercise of authority and of good governance in recent decades.

The sense of outrage across all of Irish society has been unprecedented.

Gone are the days when the Irish state bowed the secular knee to the Church authorities, though Taioseach Brian Cowen's initial over-diplomatic response to recent Vatican shortcomings was severely criticised in Dublin.

However, the Foreign Affairs Minister Micheal Martin expressed his "deep disappointment" at the lack of a response by the Pope and the Vatican to the Dublin report.

Such criticism by an Irish government minster was unheard of previously.

On the same day Cardinal Brady said, in an equally rare criticism of Rome by the Irish hierarchy, that it was unfortunate that the Vatican and the Papal Nuncio did not reply to letters from the Murphy Commission requesting information, long before the report was completed.

The Irish pressure from Church and state led to another unprecedented development when the Papal Nuncio Archbishop Giuseppe Leanza publicly expressed the Vatican's "shame, shock and dismay" at the findings of the report.

There was a feeling, however, that his comments were made too late.

All of this raises serious questions about the ability of the Church to regain the confidence of the Irish people.

Leading Dublin writer John Waters stated: "The shocking possibility arises; Ireland has been a Catholic country, but not really Christian."

Many others are asking whether the Catholic Church has been so intent on maintaining itself as an institution that it has forgotten how to live out the Gospel among the people.

This is especially true when some senior figures managed to construct a metaphysical formula to justify economies with the truth.

Another worrying factor is the apparent lack of a basic ability in parts of the Catholic Church to make basic human caring a priority.

Significantly, Archbishop Martin, a brave voice in the current mess, noted that only two of his fellow bishops rang up to ask if he was all right.

The current Catholic dilemma is also about the authoritarian nature of a male-dominated institution in which celibacy is obligatory.

This has led to an over-stretching of resources, a serious decrease in vocations and the emergence of, literally, a manpower crisis that is not going to diminish, even in the medium term.

The Catholic Church in Ireland is being forced into a radical re-appraisal of its relationships with Rome and, more importantly, with the Irish people.

Unless it exhibits a new humility, a deep repentance and a willingness to engage with the laity in a more equal partnership, this crisis of faith will continue, with diminishing returns for the faithful, both lay and clerical.