The problem was discovered around 9:30 a.m.
Amtrak crews worked to resolve the matter, and normal service had returned to the New York and New Jersey region by noon.
But some service problems remained in other affected areas, including Philadelphia and the Washington, D.C. areas until after 1:00. Officials said delays could be expected throughout the afternoon.
It wasn't immediately clear how many riders overall were affected by the service disruption.
NJ Transit spokesman Dan Stessel reported that many of the agency's lines had been affected during the outage. He said PATH trains were cross-honoring tickets in areas near New York City, while its buses were cross-honoring system-wide..