Monsignor Leo Cushley, who will be installed as Archbishop of St Andrews and Edinburgh next month, will "fully endorse" plans by the rest of Scotland's bishops to trawl church records for decades of clerical abuse.
It follows revelations Cardinal O'Brien blocked an independent inquiry into cases of historic sexual abuse that had the support of every other bishop in Scotland.
The retired Archbishop of Glasgow, Mario Conti, has revealed that the disgraced cardinal, then the president of the Bishops' Conference and who has since resigned after admitting sexual misconduct with other priests, refused to co-operate with plans to commission an independent examination of the historical cases, leading to it being shelved.
The Emeritus Archbishop told Catholic newspaper The Tablet: "It was the intention of all but one member of the bishops' conference to commission an independent examination of the historical cases we had on file in all of our respective dioceses and publish the results but this was delayed by the objection of the then-President of the Conference."
But Catholic sources have said that has already been partially undone, with current Glasgow Archbishop Philip Tartaglia opening files going back to 2006.
A spokesman for the Catholic Church in Scotland said:"It is hoped to publish these audits late in the autumn of 2013. They will contain all the aspects of the work of the eight dioceses of the Church in Scotland with regard to safeguarding and will detail any complaints made about clergy, church workers, volunteers or anyone else."
But the former head of the Church's working party on child protection, academic Alan Draper, said only an external and independent audit of historic abuse would begin to restore credibility.