Garda Commissioner Noirin O'Sullivan has denied any knowledge of an alleged campaign to damage a whistleblower's reputation.
The allegation that there was a campaign to undermine the whistleblower was made by two senior gardai in a protected disclosure to Tanaiste and justice minister Frances Fitzgerald.
It caused a political storm in the Dail, where the Taoiseach was forced to express confidence in Ms O'Sullivan and Ms Fitzgerald.
It is understood the two gardai allege that another whistleblower was the target of an orchestrated smear campaign, in the latest of a series of controversies to hit the force.
It's claimed an intelligence file was created on the whistleblower, his activities were monitored, and false allegations were made about him to the media and politicians.
Last night, a garda spokesman issued a statement insisting the Commissioner was "not privy to nor approved of" any action targeting any garda employee making a protected disclosure.
It added that Ms O'Sullivan would "condemn any such action", and reiterated her stance that any employee's concerns "will be taken seriously and the matters examined".
Earlier, at the justice committee, Independent TD Mick Wallace claimed the garda "hierarchy" is "dysfunctional" and said the latest whistleblower allegations are "pretty frightening".
Ms Fitzgerald said she couldn't go into detail on the two protected disclosures for reasons of confidentiality.
She promised to consider the matter "in a way that protects the whistleblowers and that is fair and is seen to deliver justice to all".
In the Dail chamber, Sinn Fein's Mary Lou McDonald asked the Taoiseach if he had confidence in Ms Fitzgerald and Ms O'Sullivan in the wake of the latest controversy.
Mr Kenny said he has "absolute confidence in the Minister for Justice and the Garda Commissioner".
He said he has not seen correspondence that Ms Fitzgerald has received, adding, "nor should I have".
Mr Kenny said that, ultimately, a judge may be appointed to look into the claims.
Independent TD Clare Daly asked: "What in God's name does the Taoiseach need another investigation for? Is it not patently obvious that it is beyond time for the Commissioner to go?," Ms Daly asked.
Separately, Ms Fitzgerald told the justice committee of her priorities for spending in the upcoming Budget. They include a request for funding so that "several hundred" civilians can be hired to help garda officers return to frontline duties.
She is also seeking cash to begin work on the provision of a new Forensic Science Laboratory, and referred to plans to accelerate garda recruitment. She said she expects 800 trainees will be recruited next year, and that a start would be made in doubling the numbers in the garda reserve, again subject to securing the funding.
She also wants to maintain funding for the fight against gangland crime and see increases in staff for agencies like the Charities Regulator and the Office of the Data Protection Commissioner.