NJ Transit was reporting up to 45-minute delays into and out of New York Penn Station during Wednesday morning's rush hour.
The transit agency said its rail service was disrupted by Amtrak signal issues in a Hudson River tunnel.
Rail tickets and passes were being cross-honored by PATH at the Hoboken, Newark Penn Station and 33rd Street-NY stops, according to NJ Transit.
Officials encouraged commuters to check the agency's website for the latest service information.
Amtrak did not immediately respond to a request for comment about the signal issues.
This is a developing story and may be updated.