The Taoiseach has said that there are no findings of wrongdoing against the Commissioner
The phone records of Garda Commissioner Noirín O'Sullivan are to be examined as part of an investigation into an alleged smear campaign against garda whistleblower, Sergeant Maurice McCabe.
Phone records of former commissioner Martin Callinan and those of Superintendent David Taylor, a former garda press officer, will also be examined.
Earlier, Labour leader Brendan Howlin used Dáil privilege to say he had been told the commissioner directly phoned journalists to make allegations of sexual crimes against Sergeant McCabe.
In a statement, Commissioner O'Sullivan said: " The comments made under Dáil privilege relate to allegations of the most serious nature against the Commissioner and other members of An Garda Síochána.
"The Commissioner has no knowledge of the matters referred to by Deputy Howlin and refutes in the strongest terms the suggestion that she has engaged in the conduct alleged against a serving member of An Garda Síochána.
"This is the first occasion on which the Commissioner has been made aware of the allegations made by Deputy Howlin and to her knowledge no report having been made to the Garda Siochána Ombudsman or elsewhere relating to the specific allegations.
"The Commissioner notes that a Commission of Investigation has been established, the proposed Terms of Reference for which have been published today.
"In view of the seriousness of the allegations made by Deputy Howlin and that they refer to conduct of the most damaging nature against a serving member of An Garda Síochána the Commissioner is obliged to take the unprecedented step of commenting publicly in circumstances where the Terms of Reference of the Commission have now been published.
"As previously stated, the Commission of Investigation will receive the full cooperation of An Garda Síochána and will in due course establish the truth of the matters together with all relevant facts. In the interim the members of An Garda Síochána affected by the remarks published today will receive all necessary supports and assistance having regard to the potential impact for the members concerned and their families."
Justice Minister Frances Fitzgerald announced the Commission of Investigation yesterday, following a report from retired Judge Iarfhlaith O’Neill into protected disclosures concerning the force.
The disclosures claimed that whistleblower Sergeant Maurice McCabe was the victim of a smear campaign following his attempts to bring information regarding alleged penalty points malpractice within the force into the public domain.
An Garda Síochána has said it will "co-operate fully" with the commission, which will be led by Supreme Court Judge Peter Charlton.
The Charleton Commission is being established by the Government to investigate the protected disclosure of Superintendent Taylor.
He claims he was instructed or directed by former commissioner Martin Callinan and then deputy commissioner Noirin O'Sullivan to brief the media negatively about Sergeant McCabe.
The O'Neill scoping inquiry - which recommends the Commission of Investigation - says the allegations are wholly denied, but are so serious that their truth or falsity must be established.
The Commission of Investigation has now been tasked with checking phone records of Mr Callinan, Ms O'Sullivan and Mr Taylor from July 2012 to the end of May 2014 - as well as all electronic and paper records held by gardaí on Sergeant McCabe
It will also examine specifically whether Commissioner O'Sullivan planned and orchestrated RTÉ News bulletins last May which suggested a leaked commission report was branding Sergeant McCabe a liar and irresponsible.
No timeline has been laid out for the commission of investigation - and it has discretion in relation to the scope of investigation of the matters it considers necessary.
Earlier, the Irish Examiner's Mick Clifford explained the background behind the current situation.
He explained: "Superintendent Dave Taylor was previously the head of the Garda Press Office. He was suspended 21 months ago on the basis of an allegation of having passed names to the media.
"He met Maurice McCabe for the first time last [year]. He effectively confessed to Maurice McCabe that he had been involved in a concerted effort to smear McCabe." The two officers then made protected disclosures over the claims.
Mick added: "I have to stress this is an allegation that has not been proved yet [...] But the allegation that senior management set about destroying the character of an officer who was coming forward to highlight malpractice within the force... I think it's about as serious as you can get."