In the letter, the bishops are urged not to report clerical abuse as a criminal offence.
A documentary to be aired tonight reveals the contents of the letter and also claims that, on at least two occasions, the Vatican stepped in and stopped attempts by Irish bishops to defrock abuser priests.
Last month, details of one of those occasions was made public when a High Court order finally allowed the full publication of a previously censored chapter in the Murphy Report on the Dublin Archdiocese.
That revealed that when bishops made moves to dismiss paedophile priest Tony Walsh, the Vatican instead sought to send Walsh to serve 10 years in a monastery.
Tonight’s RTÉ programme, Unspeakable Crimes, shows Walsh went on to abuse another child after a Church court recommended that he was laicised because Rome insisted on a long, drawn- out appeal of his case.
In the programme the mother of that child, who didn’t wish to be named, points the finger directly at the Vatican for the abuse of her son.
The programme also reveals how one Irish archbishop, who can’t be named for legal reasons, did threaten to resign because of a case in the 1990s.
The DPP declined to prosecute the priest in question, but the Irish archbishop, through the Church tribunal, recommended that the priest be dismissed from the clerical state.
When the Vatican overturned the decision of the tribunal, the documentary reveals that it is believed the archbishop threatened to resign if the priest was to be reinstated.
Abuse survivor and spokesperson for the Voice of the Faithful organisation Bryan Maguire said the 1997 letter sent to the Irish bishops changes the way he feels about the clerical abuse issue.
He said: “It certainly puts a different complexion on the way in which the Irish bishops acted and points a finger right back to Rome.
“At root what we’ve got is not just abusive priests and bishops that cover up, but an entire system that has enabled and facilitated those bishops and priests.
“What we want is for the Church to take a mirror to itself and not to just push the problem down to a local problem,” he added.