The Taoiseach said it was hoped that all phases of the Luas light railway system would be completed next year.
Mr Ahern said the reason there was a difference in costs and cost-analysis for the metro was that they related to different proposals and projects.
"It is natural that there would be different cost structures in such an event," he added.
The matter was raised by the Green Party leader, Mr Trevor Sargent, who accused the Government of a lack of competence and cohesion.
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"This is being increasingly revealed in the disagreements between high level members of Fianna Fáil," Mr Sargent said.