The issue of an apology to Ms Nora Wall, whose rape conviction was quashed, had still to be addressed, the Taoiseach said.
Mr Ahern said the Director of Public Prosecutions and the Attorney General had commented on the matter. "Admittedly, a formal apology has not been made."
The Taoiseach was replying to the Labour leader, Mr Ruairi Quinn, at Question Time.
The Fine Gael spokesman on justice, Mr Jim Higgins, said the State's counsel had failed to recall the DPP's instruction that a specific witness was not to be called. "Will the Taoiseach agree that in a case where an innocent person is wrongly convicted, we are not talking about a weakness in communication but downright incompetence?",
Mr Ahern said he did not want to add anything other than what the new DPP had stated in his report. "According to the outgoing DPP and the incoming DPP, I must reflect that to the best of their knowledge it is the first time in 25 years this has happened. It was a series of substantive errors." Pressed by Mr Quinn to say if those involved would be paid for their incompetence, Mr Ahern said what was cleared by the DPP was not a matter for him.
The Fine Gael leader, Mr John Bruton, said the State and the media had done an injustice to the accused and should apologise.