The MTA said most Manhattan-bound Long Island Rail Road trains were being diverted to alternate terminals during Tuesday morning's rush hour due to a broken rail in an East River tunnel.
Direct service from Jamaica to Penn Station was suspended, transit officials said. LIRR trains were being diverted to other locations like Long Island City, Atlantic Terminal and Grand Central so riders could get on the subway.
Track capacity was also limited because of ongoing Amtrak tunnel work related to Penn Station access, according to the MTA.
Officials said LIRR tickets would be cross-honored on the subway Tuesday morning.
The MTA said to expect delays, cancellations and crowded trains, but did not say how long the disruptions would last. They appeared resolved by late Tuesday morning, according to the agency's service app.
At an unrelated press conference, MTA Chair Janno Lieber said the agency has known such cascading disruptions are a possibility as Amtrak conducts the tunnel work.
"We keep pushing Amtrak to prepare for these kinds of downside scenarios, and you know what, they were prepared, to Amtrak’s credit, and we minimized the harm to railroad customers," he said.
Ramsey Khalifeh contributed reporting. This story has been updated with additional information.