Blackrock College and Belvedere College have been rocked by admitted allegations of sexual abuse that was not tackled by management.
Cabinet decided today to establish the investigation, which is short of a a public inquiry.
A report is going out to survivors today, former teenage pupils who are now in their late 50s and 60s.
The terms of reference are to be drawn up for the inquiry which officials stressed will have strong powers, with representatives of the Spiritan order, which ran Blackrock, and the Jesuits, controlling Belvedere, expected to fully cooperate.
A scoping report that went to Cabinet made harrowing findings, sources said, with many other religious-run schools also the subject of allegations.
The scale of the alleged abuse opens a new front from Diocesan sexual abuse and predations in residential institutions, indicating clergy were committing crimes across the board where they had access to the vulnerable.
“Multiple” schools are named in the scoping report, with ministers said to be shocked at the scale of the problem — although similar sexual abuse scandals across Catholic-run schools have been uncovered in other countries.
The report could be published tonight, once it has gone to recognised survivors of the suffering, sources said.
Some in Government believe this could be "just the beginning" of a much wider issue that might ultimately have to be investigated.
Taoiseach Simon Harris said today before Cabinet: “Survivors will be the first to know the next steps the Government takes in relation to any statutory inquiry.”
The investigation is expected to be headed up by a senior counsel or a retired judge. It is not yet known if any of the formal sessions will be held in public.
Many of the abusers are dead, however, given the lapse of time, including the sadist and paedophile Joseph Marmion SJ, who carried out serial crimes in at least three Jesuit-run schools.
Many other abusers are thought to have offended at more than one school, and the investigation is expected to look at whether they were shunted from one school to another once allegations came to light.
That was the process seen at diocesan level, and even with episcopal offenders like the late Bishop Eamon Casey of Galway, where the idea of removing him from the cathedral crypt is still under consideration.
Mr Harris said Minister for Education Norma Foley had reviewed the scoping report that had been carried out. It is understood she then brought her concerns to him — and Mr Harris discussed it in turn with his fellow Coalition party leaders, Micheál Martin and Roderic O’Gorman, on Monday night.
“She (Minister Foley) and I and everyone in Government have said that, in terms of the next steps, the people we want to know first are the survivors,” he said.
“The minister has been engaging with their representatives.”