The archbishop of Dublin has said the Irish prime minister's attack on the Catholic church following a report on child sex abuse in the country should be a wake-up call for clergymen.

Enda Kenny launched his unprecedented attack on the Vatican in the Irish parliament, accusing it of downplaying the rape and torture of Irish children by clerical sex abusers.

He said the recent Cloyne report had exposed an attempt by the holy see to frustrate the inquiry into child sex abuse just three years ago and illuminated the "dysfunction" and the elitism still dominant in the Vatican.

Archbishop Diarmuid Martin – close to tears in an interview on RTE Television – said the only way all allegations, abuse and cover-ups could be exposed was through invasive audits of each diocese. "I'm very disappointed, annoyed," he said.

"What do you do when you've got groups, whether in the Vatican or in Ireland, who try to undermine what is being done or simply refuse to understand what has been done?"

The archbishop said the diocese of Cloyne had ignored Vatican policy issued in 2001 by the then Cardinal Joseph Ratzinger, now Pope Benedict.

"What does that say? What sort of a cabal is this that is in there [Cloyne]?" He added: "If they think that by not getting at the truth they are helping the church, the statement in today's Dail should teach them a lesson."

Kenny had told the parliament that the Vatican seemed more interested in upholding the power and reputation of the Catholic church than in confronting the abuse of Irish children by its priests and religious orders.

He said that the Vatican's attitude to investigations in Cloyne, which covers county Cork, was the "polar opposite of the radicalism, the humility and the compassion that the church had been founded on".

He said the rape and torture of children had been downplayed, or managed, to uphold instead the institution with its power and reputation.

One of the most damning findings of the report was that the diocese failed to report nine out of 15 complaints made against priests, which "very clearly should have been reported".

This latest report, coming after a string of inquiries into Catholic clerical sex abuse across Ireland, has set the present Irish government on a collision course with the church not only in the republic but at its global headquarters in the Vatican City.

Vatican spokesman Fr Federico Lombardi, speaking in a personal capacity, had said that there was nothing in the advice given by the papal nuncio to Ireland in 1997 to encourage bishops to break Irish laws.

He said that the Vatican's advice to Irish bishops on child protection policies could not be interpreted as an invitation to cover up abuse cases.

This drew sharp criticism from Ireland's justice minister, Alan Shatter, who described the Vatican spokesman's argument as disingenous. Some Irish parliamentarians have called on the Fine Gael-Labour coalition to expel the papal nuncio from Ireland in protest at the Vatican's attittude to the allegations in the Cloyne diocese.