Taoiseach Enda Kenny has said he did not regret his unprecedented attack on the Vatican after it rejected his claims that it tried to frustrate an inquiry into clerical child abuse.

In its formal response to the Government in the wake of the latest church abuse scandal, the Holy See said that it in no way hampered or interfered with the inquiry into abuse cover-ups in the Cloyne diocese.

Mr Kenny launched a blistering attack on the Vatican in the Dáil, claiming that the probe exposed a dysfunctional, elite hierarchy determined to frustrate investigations.

But the Holy See said the Cloyne Report did not back up the Taoiseach’s allegations.

The Vatican said: “In particular, the accusation that the Holy See attempted ’to frustrate an inquiry in a sovereign, democratic republic as little as three years ago, not three decades ago’, which Mr Kenny made no attempt to substantiate, is unfounded.”

The Cloyne Report, published in July, was the fourth major report in six years into the church’s cover-ups of clerical abuse.

The Co Cork diocese was the latest arm of the church to be exposed, with former bishop John Magee, a Vatican aide to three Popes, singled out for misleading investigators and “dangerous” failures on child protection.

His resignation was accepted by Pope Benedict last year.

Opening a special Dáil debate a week after the report’s publication, Mr Kenny hit out at the Vatican and accused the church of downplaying the rape and torture of Irish children by clerical sex abusers.

Mr Kenny said he did not regret making the speech.

“I made my statement to the Dáil, and obviously the question being asked by the Tánaiste on behalf of the Government was to have the Vatican respond in respect of a statutory commission of inquiry arising from the Cloyne situation,” the Taoiseach said.

But Fr Federico Lombardi, director of the Holy See’s press office, rejected Mr Kenny’s Dáil comments.

“We do not understand what was in the mind of the Prime Minister,” he said.

The Vatican claimed it never hampered or interfered in the inquiry into child sexual abuse cases in the diocese.

“Furthermore, at no stage did it seek to interfere with Irish civil law or impede the civil authority in the exercise of its duties,” the statement said.

The 25-page Vatican statement was issued after Foreign Affairs Minister Eamon Gilmore demanded answers from the Holy See on claims that it allowed priests to ignore mandatory reporting guidelines on suspected child abusers within the church.

It said the Holy See was sorry and ashamed for the “terrible sufferings which the victims of abuse and their families have had to endure”.

“The Holy See is deeply concerned at the findings of the commission of inquiry concerning grave failures in the ecclesiastical governance of the Diocese of Cloyne and the mishandling of allegations of abuse.”

The Vatican became embroiled in the latest Irish church scandal after revelations about a 1997 letter, from the then papal nuncio to Ireland Archbishop Luciano Storero to Irish bishops, a year after reporting guidelines were enforced to enhance child protection.

The correspondence stated that the bishops’ policy was “merely a discussion document” and that the Vatican had serious moral and canon reservations about mandatory reporting of clerical abuse.

But the Vatican says that taken out of context, the comments in the letter to Irish bishops “could be open to misinterpretation, giving rise to understandable criticism.”

It said the description of the bishops’ policy as a study document was not a dismissal of the serious efforts being undertaken to address the child abuse problem.

It said senior church figures wanted to ensure that “nothing contained in it would give rise to difficulties should appeals be lodged to the Holy See”.

The Holy See also denied that bishops sought recognition from Rome for its so-called framework document.

“In the light of the findings of the Cloyne Report, the basic difficulty with regard to child protection in that diocese seems to have arisen not from the lack of recognition for the guidelines of the framework document but from the fact that, while the diocese claimed to follow the guidelines, in reality it did not,” the Vatican said.

The Holy See said the response of the Congregation for the Clergy, through Archbishop Storero, was not a rejection of the framework document, but an invitation to bishops to re-examine it carefully.

But Mr Gilmore branded the arguments put forward by the Vatican legalistic and technical.

“The Government’s concern was never about the status of the church documents but rather about the welfare of children,” Mr Gilmore said.

“In relation to the Framework Document, I remain of the view that the 1997 letter from the then nuncio provided a pretext for some to avoid full co-operation with the Irish civil authorities.

“The sexual abuse of children is such a heinous and reprehensible crime that issues about the precise status of documents should not be allowed to obscure the obligation of people in positions of responsibility to deal promptly with such abuse and report it.”

The Vatican also said the Congregation was not forbidding mandatory reporting, “or in any way encouraging individuals, including clerics, not to cooperate with the Irish civil authorities, let alone disobey Irish civil law”.

The Vatican said that as the Irish government had not made mandatory reporting of suspected abuse cases law at that time, it was difficult how concerns raised in Archbishop’s Storero’s letter could be construed as having subverted Irish law.

The Government has now committed to tough new child protection measures in the wake of Cloyne, including making it an offence to withhold information about crimes against children and introducing new vetting to allow “soft information” transfers.

The Holy See said while it cannot comment on the proposed legislation, it welcomes and supports attempts to protect children.

But it signalled there could be difficulties with plans to ensure allegations made in the confessional are reported to civil authorities.

Clerical abuse survivors said the Vatican’s response was another attempt to absolve itself of responsibility for abuse cover-ups.

But all-Ireland primate Cardinal Sean Brady said it conveyed the Holy See’s profound abhorrence for the abuse, and sorrow and shame for victims’ sufferings.