Minister Eoghan Murphy is ordering councillors to delete part of a major development plan after being told it will scupper MetroLink.
The National Transport Authority (NTA) has warned the plan, finalised in defiance of the local government minister's prior warnings, makes it impossible to take MetroLink to the planning stage.
But the councillors insist it is their duty to retain their plan to force more ambitious public transport investment.
The row erupted after members of the Eastern and Midland Regional Assembly, which represents 12 local authorities in Leinster, said two underground spurs should be added to MetroLink in Dublin to serve University College Dublin and the suburb of Knocklyon.
They included the objective in their new Regional Spatial and Economic Strategy (RSES) which guides development in the region until 2031, despite warnings it was not aligned with the Government's more modest plans and so breached the Planning and Development Act.
Mr Murphy has now issued notice of a ministerial direction to change the RSES. He is backed by the NTA which was highly critical. "The inclusion of the additional metro lines in the RSES creates a major inconsistency," deputy chief executive Hugh Creegan wrote in response.
He said until the RSES was amended, "it is no longer possible to progress the current MetroLink project through a planning approvals process".
He continued: "If the MetroLink project were required to align with the RSES proposal, it would have to be fundamentally changed." He said this would delay the project by between three and four years and potentially longer.
The planning regulator and Department of Transport also support Mr Murphy's stance.
The RSES, approved by a majority vote in May, also includes objectives to extend the Luas to Booterstown, Hazelhatch and Blessington, provide a new rail commuter route to Navan and greatly extend electrification of lines.
Councillors also defied warnings about these, arguing they had a legal obligation to reduce carbon emissions through the provision of more public transport.
They said the Greater Dublin Area Transport Strategy, with which their plan is meant to align, would likely lead to an increase in greenhouse gas emissions.
Councillors and the public have until the end of today to make submissions to Mr Murphy before he finalises his direction.
Fingal Councillor David Healy said he would be arguing against changing the RSES: "The assembly and the NTA are not bound to keep copying each other in their respective strategies or else nothing will ever change."
Jim Conway, assembly director, said it was up to the elected members to decide how to proceed. "We advised them on Government policy and they exercised their right to vote against that advice."