The Taoiseach has blamed the high number of allegations of abuse and the legal challenges taken by alleged abusers for the delays experienced by the commission to inquire into child abuse.
In his first public comments since Ms Justice Laffoy resigned as chairwoman of the commission earlier this week, Mr Ahern acknowledged there had been tensions between the Government and the commission. He said he understood that delays had frustrated and annoyed the Commission but added: "Obviously they are not happy, but neither am I."
The Fine Gael leader, Mr Enda Kenny, and the Labour Party leader, Mr Pat Rabbitte, yesterday called again for the immediate publication of Ms Justice Laffoy's resignation letter.
However, a Government spokeswoman repeated that it would not release the letter until at least after next Tuesday's Cabinet meeting, by which time it hopes to have prepared a detailed response to the judge's strong criticisms of Government actions which delayed the commission's work.
Mr Ahern said yesterday that when the commission was set up he had expected its work to be complete within a few years, and had not anticipated that so many cases of alleged abuse would emerge. There were now 1,700 cases, and there could be more.
"I have to say frankly that I never thought that we were going to get into 1,700 trials or maybe even more than that," he said.
The Government's intention in reviewing the operation of the commission was to find a way to deal with the huge volume of cases so that he could honour a pledge he made to abuse victims in 1999.
"In May 1999 I made the apology on behalf of the State, having spent a considerable amount of time listening to the victims, and they persuasively convinced me that this was an issue that needed to be comprehensively addressed.
"I promised them then and still do that however we manage to do it we will get to the end of it," the Taoiseach said.
The State's response had been to set up three separate arenas in which the issues would be addressed. There was the Laffoy Commission's investigation committee which was investigating allegations, the commission's confidential commission where abuse victims could tell their stories in confidence and the separate redress board which was making compensation awards.
"The compensation tribunal is working well, the confidential unit is working well, the investigation unit isn't working well and it's not working well for a whole host of reasons," Mr Ahern said.
"The reason we had a review was to see if we could make that work better, to try to find a way that we could deal with this efficiently and effectively and speedily, and quite frankly we haven't succeeded in doing this."
He said there had been a Supreme Court judgment in July that impinged on how the commission would operate, and another judgment was awaited in a case taken against the commission by the Christian Brothers.
In the case decided in July Prof Patrick Meenan (86) had successfully challenged an order by the commission that he give evidence before it in relation to the conduct of vaccination trials in 1960 and 1961 in children's homes. Prof Meenan had argued that he should not have to appear on grounds of his age and ill-health.
The Christian Brothers meanwhile are arguing that deceased, incapacitated or untraceable brothers or former brothers should not be named by the commission.
Mr Ahern said the Government was not delaying its review of the commission's modus operandi. "We are ready with the results of the first review, and the second review is only the second stage of that," he said.
" We are only delaying because we are waiting for these judgments to come through so we can see where we can get." People were entitled to take actions against the conduct of the commission if they felt their constitutional rights were being denied them.
But the cases were "far more legalistic and far more complex than we ever envisaged".