The agency is also looking into possible impacts on the project.
The rail link is projected to be completed in 2023 and cost nearly $11 billion. In 2006, the agency estimated the East Side Access project could be finished by the end of 2013 at a cost of $6.3 billon.
Work has been temporarily suspended at the Harold Interlocking in Sunnyside while the cause of the ground collapses is investigated. The location is just east of the tunnels that bring the LIRR into and out of Penn Station.
The MTA said it expects the investigation to be completed in about two weeks.
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