The delays, which began just as the morning commute was ending, were due to an investigation into an unattended bag on the bridge, Metro-North said via Twitter.
Police cleared the scene at 138th Street and train service was resuming through the area, Metro-North said.
"Customers should anticipate residual delays of 60 to 90 minutes. We thank you for your patience," Metro-North said.
No other details were released on the incident.
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