The recommendations in the Police Ombudsman's report on the Omagh bombing need to be carefully examined, the Taoiseach said in Dublin.
Speaking to reporters after a session of the Forum on Europe, Mr Ahern said: "It is a very important report and its recommendations have to be examined very, very carefully."
He was non-committal on whether the Omagh investigation should be taken out of the hands of the Police Service of Northern Ireland but said the findings were specific and "disturbing". There had been "a very formidable team behind that report".
Asked if the killing of the loyalist William Stobie would inhibit the inquiry into the death of the solicitor Pat Finucane, Mr Ahern said: "We have not changed our position on that." Finucane and other inquiries had to be brought to a conclusion, he said.
The Minister for Foreign Affairs, Mr Cowen, said in a statement that the Ombudsman's report "clearly raises issues of concern about the police investigation into the Omagh bombing. It is important that these concerns be fully addressed".
Meanwhile, Downing Street has confirmed Prime Minister Tony Blair's continuing confidence in the Chief Constable of the Police Service of Northern Ireland, Sir Ronnie Flanagan.
Mr Blair reported to the cabinet yesterday on the bitter fallout from the Police Ombudsman's report into the RUC's handling of events before the Omagh bombing in August 1998 and the subsequent investigation into the worst terrorist atrocity of the Troubles.
The Prime Minister's official spokesman said Mr Blair told cabinet colleagues there had been no specific warning of a bomb in Omagh on August 15th, and that it was right and proper that Sir Ronnie be given time to respond to Ms Nuala O'Loan's report.
Mr Blair welcomed "the remarkable achievement" of the new Policing Board in resolving the vexed question of symbols for the new police service and spoke of "a real opportunity for a new era in policing in Northern Ireland, not least thanks to the leadership shown by the Chief Constable", who had played "an absolutely vital part in the peace process at critical and difficult times."
The North's Police Federation has withdrawn its invitation to Ms O'Loan to its Christmas party. A federation spokesman said the withdrawal of the invitation was "nothing personal", but that the presence of the Ombudsman or that of her staff would "put a dampener on proceedings".