If the Treaty of Nice had posed a threat to "fundamental Irish interests", the Taoiseach would not have agreed to it, he has said.
Mr Ahern claimed opponents of the treaty were "deliberately misrepresenting what is involved".
He accused anti-Nice campaigners of falsely suggesting that the enhanced co-operation provisions of the treaty would mean the big states rushing ahead of the smaller ones. "Nothing could be further from the truth," he said.
"Enhanced co-operation can only be used as a last resort. It cannot be used in any circumstances for security or defence issues. It cannot undermine the internal market or distort competition."
There could be no question of leaving anyone behind, he added.
Dismissing suggestions of a divide between big and small states, he said Ireland had often formed alliances with larger member states on vital issues. "For example, France is a key ally on the CAP," Mr Ahern said.
Meanwhile, the Green MEP for Leinster, Ms Nuala Ahern, said Ireland's automatic right to an EU commissioner had to be confirmed before the referendum. "The automatic right to a commissioner is one of the planks by which the European Union is legitimated in the eyes of citizens, particularly in small countries like Ireland."
The Government should "press the case for the Council of Ministers to agree to the automatic right to a commissioner for all. This could be agreed at an EU council and the Government should be actively seeking a solution on this most important issue for Ireland".
Ms Ahern said the Government would be "knocking at an open door" on this issue during the current Danish presidency and that the European Commission itself was also sympathetic to such a solution. "Taoiseach Bertie Ahern was very wrong to go to the Council of Ministers after the Nice Treaty rejection without proposals such as this, which are in the best interests of Ireland.
"It is clear from sources in Brussels that it is widely believed that the Convention on the Future of Europe was a direct result of the Irish 'No', as it underlined how out of touch the EU was with its citizens."