Two senior ministers have said that only the Garda Commissioner can explain the discrepancy between her stated support for Sgt McCabe and the transcript presented on RTÉ's Prime Time Tuesday night.

Speaking to the Irish Times Inside Politics podcast, Government Chief Whip Regina Doherty said, "There's definitely an inconsistency about the very very clear statement the commissioner made two days ago and what was leaked illegally last night.

“ For all our sakes.... and most particularly for the commissioner’s sake there needs to be clarity. I think in fairness the commissioner is the person that can give clarity on that, nobody else can,” Ms Doherty said.

The commissioner, Noirín O'Sullivan, is under pressure after details emerged of an exchange between Ms O'Sullivan's senior counsel Colm Smyth and Mr Justice O'Higgins.

According to leaked transcripts of the commission hearings, seen by RTÉ, early in the hearings Mr Smyth had said his "instructions from the commissioner" were "to challenge the integrity . . . of Sgt McCabe".

However, on the morning Ms O’Sullivan was to give her evidence, Mr Justice O’Higgins sought further clarification and Mr Smyth informed him his “instructions at all times were to challenge the motivation and credibility of Sgt McCabe”.

Mr Smyth said it was an error on his part when he had earlier stated he was instructed to challenge Sgt McCabe’s “integrity”.

Minster for Justice Frances Fitzgerald told the Dáil on Wednesday morning that she expects the commissioner to clarify matters surrounding her approach to the handling of the whistleblowers claims' at the O'Higgins commission.

She also said that the commissioner will release further information on the commission if legally possible.

“Of course, I will have ongoing discussions with the Garda Commissioner and, if it is feasible and legal for the commissioner to put further information into the public arena, I have no doubt she will do that,’’ Ms Fitzgerald said.

The commissioner had made some of the points to her which she made later in a public statement, she added.

Ms O’ Sullivan had accepted the report and Sgt Maurice McCabe’s bona fides and that he had never suggested malice was a motivation.

Ms Fitzgerald was asked by Sinn Féin leader Gerry Adams if she had asked the commissioner what instructions she had given to her legal team at the commission relating to Sgt McCabe.

He also asked if Ms Fitzgerald had raised with the commissioner whether two Garda officers had claimed Sgt McCabe had said to them he had acted with malice.

The Minister said she was very aware of her duties to the House.

She added there had been a commission of investigation which interviewed 94 witnesses. “Some of the allegations made two years ago have been found not to be correct,’’ she added.

“It is very important we do not try and reinvent the wheel here in relation to some of issues dealt with very thoroughly by the commission of investigation.’’

Ms Fitzgerald said there had been a “very thoughtful and thorough’’ report.

“I think it behoves us all to look at it in its entirety,’’ she added.

Independent TD Mick Wallace said on Wednesday nothing had changed within the Garda and their treatment of whistleblowers.

Speaking on Newstalk Breakfast, he said: “Nothing has changed. People thought they would get change when the former minister and former commissioner went.

“Noirín O’Sullivan and Frances Fitzgerald were fresh new faces, but with the same old way of doing things.

“The commissioner came out and said that anyone who raises issues would be fully supported and that’s not true,” Mr Wallace said.

"Other whistleblowers have been treated the same as Maurice McCabe and John Wilson were five years ago. Nothing has changed."

Mr Wallace said that what was being said in public was completely different to what is going on behind the scenes, and was disappointed that there was no apparent change in how whistleblowers are dealt with.

“The fact that she (Noirín O’Sullivan) was prepared to go through this process to undermine the credibility of Maurice McCabe shows that the system has not changed.

“If her legal team was acting outside her remit that beggars belief. If she’s innocent, she can come out and tell us what happened.”

Mr Wallace said that Ms Fitzgerald has to play a more active role in finding out what happened.

“If the commissioner doesn’t act, the Minister could find herself being brought down like Shatter was,” he said.