Tanaiste Eamon Gilmore is to seek a meeting with the Pope's ambassador to Ireland over Rome's role in the Cloyne scandal.
The report into the handling of clerical sex abuse allegations in the diocese branded the Vatican "entirely unhelpful" over its dismissal of mandatory reporting guidelines as "merely a study document".
Justice Minister Alan Shatter said the intervention by the then Papal Nuncio - whom he described as an ambassador from a foreign state - was unfortunate and unacceptable when the country had been assured the church had implemented new child protection guidelines.
Describing it as a matter of some seriousness, Mr Shatter said it was a matter for the Tanaiste and Foreign Affairs Minister to "have a conversation" with the Papal Nuncio.
It is understood officials were keen to hold talks as early as today but no date for the meeting has been arranged.
A spokesman for the Department of Foreign Affairs said: "On behalf of the Government the Tanaiste will be bringing the report to the attention of the Vatican authorities and he will be meeting with the Papal Nuncio."
Children's Minister Frances Fitzgerald also turned on the Vatican for being "singularly unhelpful" over the scandal.
"When the Irish church sought to apply guidelines to prevent it happening again, the Vatican told its clerics that those guidelines were not what they appeared," she said.
Ms Fitzgerald said the reference to the official Irish Church policy on dealing with suspected paedophile priests as a study document ensured that, as the study continued, so did the child abuse.
The Cloyne report found the response from the Vatican effectively gave carte blanche to Bishop John Magee to ignore guidelines and offered "comfort and support" to senior clerics such as Monsignor Denis O'Callaghan who dissented on the guidelines for alleged abuse.
The Papal Nuncio wrote the secret letter to all Irish bishops in 1997, a year after the framework document on child protection was introduced.
In it he also wrote: "In particular, the situation of 'mandatory reporting' gives rise to serious reservations of both a moral and a canonical nature."
Caoimhghin O Caolain, Sinn Fein spokesman on children, demanded the Government call in the Papal Nuncio to answer questions about the affair.
"This is a damning indictment of the role of the Vatican. The Vatican is not just a Church bureaucracy - it is a sovereign State with which the Irish State has diplomatic relations," he said.