The Government "is committed to decentralisation and the process that has been outlined", the Taoiseach, Mr Ahern, told the Dáil as the Opposition called for a review of the proposals.
He said there would be no "knee-jerk reaction that we will not do anything".
Decentralisation "must work, it must be organised and difficulties will come up". If people look for reform "but give up as soon as someone says they do not like it, then the country would not be where it is today."
The Labour leader, Mr Pat Rabbitte, claimed the Progressive Democrats had campaigned in the local elections on the basis that decentralisation was a "Fianna Fáil idea".
He said decentralisation as announced was "simply unworkable". It was a "daft, old-fashioned Fianna Fáil stroke".
It might be "good for some local towns, but bad for Ireland. Governance will not be possible. It will lead to the destruction of specialist agencies. You cannot seek to relocate professional staff in a particular niche area, and replace them with generalist civil servants from another area.
"If Ministers are going around beating their breasts and saying they have learnt lessons, what lesson has the Taoiseach learnt in respect of decentralisation?"
Denying it was "daft", Mr Ahern said "the reality of the city, the national spatial strategy and balanced regional development is that Dublin cannot continue indefinitely to grow at the rate of the last 10 to 15 years. That is not a good thing. "The Central Fisheries board was on the banks of the Tolka for years, protecting the pinkeens. What is the sense in that?"Specialist agencies could successfully move. "The CSO has our best statisticians. Its representatives were in my office a decade ago saying they could never leave Dublin, but they are now happy in Cork."
Last night Mr Dom McLave, IT systems manager with the Central Fisheries Board and shop steward with SIPTU, accused the Taoiseach of being "arrogant in the extreme".
Mr McLave said he had received 30 phone calls in three hours from angry staff at the board's headquarters in Glasnevin, Dublin following Mr Ahern's comments.
"People are going through enough trauma at the moment without hearing such glib comments from the Taoiseach.."
Mr McLave said he will ask SIPTU to take the matter to the "highest level".
