The Metropolitan Transportation Authority is blaming so-called risk factors for a delay in the completion of the East Side Access tunnel until 2019.
The mega-project, which will link the Long Island Rail Road to Grand Central Terminal, was originally supposed to be complete by late 2015.
MTA officials have now pushed that deadline back four years.
In a statement, officials did not specify the risk factors, but said the issues came up during a preliminary analysis of ongoing construction.
The agency is working with its partners to update a funding agreement that would reflect the new timeline.
The $7.4 billion project will accommodate more than 500,000 commuters.