(Bloomberg) -- Trains into New York City operated by both New Jersey Transit and Amtrak are back to running on a normal schedule, with residual delays, after an Amtrak train broke down, disrupting the morning commute.

A commuter train broke down in the North tube of the tunnel that runs under the Hudson River connecting Manhattan to New Jersey. The train was removed as of 9 a.m. and scheduled train operations have resumed, according to Jason Abrams, an Amtrak spokesperson. 

Amtrak trains were running on delays of up to 90 minutes after the breakdown and traffic was blocked in and out of New York’s Penn Station — the nation’s busiest railway station.

A notification sent by New York City’s emergency alert system said that customers on both train operators should “expect extensive delays and possible cancellations between New York and New Jersey.”

The rail structure that runs up and down the US East Coast comes to a choke point at the border of New York and New Jersey. Both NJ Transit and Amtrak trains have to pass through a single, century-old tunnel to enter Manhattan. One minor disruption to that narrow passage can ripple across both agencies and cause headaches for commuters.

The long-awaited $16 billion Gateway project — which is slated to secure the final signatures for federal funding by the end of the summer — is designed to alleviate the congestion by building a new tunnel and renovating the existing one. 

“Unfortunately, today hundreds of thousands of commuters are being reminded, the hard way, of how urgent the Gateway Hudson Tunnel is to ensuring these crippling delays stop happening,” Gateway Development Commission spokesperson Steve Sigmund said in a statement. 

--With assistance from Cristin Flanagan.

(Updates with train service information, statement from Gateway.)

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