An independent review initially considered adding an historic complaint against whistleblower Sgt Maurice McCabe to the terms of reference of the O'Higgins commission of investigation, but decided not to after reviewing the garda investigation files.
The historic allegations of sexual assault, made in 2006 by Miss D, ended in a direction from the DPP against prosecution as there was no evidence that any crime had occurred.
The Charleton tribunal is examining whether unjustified grounds were inappropriately relied upon by former garda commissioner Nóirín O'Sullivan to discredit Sgt McCabe at the O'Higgins Commission of Investigation.
Michael Flahive, an assistant secretary in the department of justice, said, in his evidence to the tribunal, that senior counsel Sean Guerin SC had conducted a "paper review" of existing reports and documentation on cases which Sgt McCabe had highlighted.
Following the publication of the Guerin Report in 2014, an Independent Review Mechanism (IRM) was set up with two senior and five junior counsel to consider what cases should be referred to a Commission of Investigation.
Mr Flahive said it was recognised that including the Miss D case in the terms of reference for the O'Higgins Commission "could be very problematic".
"Rightly or wrongly, fairly or unfairly, it would have been seen as having the effect of putting Sgt McCabe on the back foot with the investigation," Mr Flahive said.
Mr Flahive said he asked if the lawyers at the IRM, who had only seen a letter from Miss D, could also see the Garda files for the case. This was organised, and after reviewing the files the IRM decided against adding the Miss D case.
The witness agreed with Michael McDowell SC, on behalf of Sgt McCabe, that "it would have been a huge problem for Sgt McCabe if he was both quasi-defendant and somebody to give evidence" at the Commission.
Mr Flahive said the the terms of reference for the O'Higgins commission "are almost verbatim as recommended by Sean Guerin," except for three small technical differences.
Mr Flahive said that it was clear in his mind that it would not have been possible, or even proper, for the minister to intervene in relation to the garda commissioner's legal instructions at the Commission.
Tribunal chairman Mr Justice Peter Charleton asked Mr Flahive what he would have done if he had been told that someone was to "deploy as a weapon against Sgt McCabe the actual allegation of abuse."
Mr Flahive said he never for a second thought that would happen, but if he had, he would have had discussions with the department secretary general, the minister, and the attorney general, to see what could be done.
Mr Michael Dreelan, an official in the Attorney General's office, told the tribunal he first learned of the Miss D allegations when he was contacted by solicitor Annmarie Ryan on 15 May 2015.
Mr Dreelan said his prior knowledge of the case was "absolutely zero." He said he understood that although the DPP had directed no charges in the case as there was no evidence of any crime, the investigation had "a very profound impact on Sgt McCabe, and arising from that, that had caused a change in Sgt McCabe's behaviour and in his relationship with the force".
"I was informed that An Garda Síochána would put it to Sgt McCabe that he was motivated to raise the issues before the O'Higgins Commission by a sense of having been treated unjustly," Mr Dreelan told the tribunal.
Mr Dreelan wrote an email on what he was told by Ms Ryan, which he forwarded to his superior. He said he was aware that the Department of Justice would have to be informed "at an appropriate level".