The National Transport Authority has said that there is little point in carrying out underground preparatory works on the Metro and DART due to uncertainty over funding.
The Rail Procurement Agency is seeking permission for the Luas BXD line and has said that the 10-year planning permission for the other projects could lapse before finance becomes available.
The agencies were responding to a request for information from An Bord Pleanála.
The Metro North and DART Underground lines have already received planning permission.
The underground lines were planned to be built first but were deferred because of their combined estimated cost of up to €5bn.
Luas bridge construction to continue
Dublin City Council is proceeding with the construction of a new bridge that will allow the Luas link up despite uncertainty about the project.
An Bord Pleanála had expressed concern of the timing of the Luas project as it could interfere with future developments of the Metro North and Underground DART lines.
The Marlboro St bridge is designed to cater for the Luas BXD link up line between the Green and Red routes.
But that was meant to be completed after the Metro North and DART Underground projects.
Those projects were shelved by the Government, which gave the go ahead to the Luas BXD - it will cost around €300m.
An Bord Pleanála was concerned that the new Luas line could interfere with future development of the underground projects.
But in a statement published today, the National Transport Authority said it believed the BXD should go ahead now.
A decision on the Luas line is expected from the planning authority this summer.
An Bord Pleanála also received an independent report on the feasibility of the BXD line running without overhead cables in areas such as Trinity College and O'Connell St.
The report from consultants Systra said it would cost nearly €19m to retrofit the Red Line trams and build new ones with their own power.
The Rail Procurement Agency has said that it is opposed to this on grounds of cost and also because it would mean trams would not be interchangeable on the Green and Red lines.