Trains began being impacted by the fires around 2:45 p.m., just before the start of the evening rush.
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At one point New Jersey Transit said service was suspended on its Northeast Corridor Line between New York Penn Station and Trenton.
It led to a commuting hassle for train riders as large crowds gathered at Penn Station and were left to figure out how to get home after the shutdown.
Rail service has since resumed with "significant delays" in both directions between New York Penn Station and Trenton. Westbound service will bypass Metuchen, Edison and New Brunswick.
Customers are being advised to transfer at Princeton Junction for eastbound service back to these stations.
Frustrated Amtrak travelers at 30th Street Station had to make alternate plans to get to their destination.
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"Flights to Boston are now $2,000. We have to get there tonight, so same day flights are hard to come by," said Stephanie Roundy of South Philadelphia.
Cindi Buckwalter was trying to get to Washington, D.C.
"They stopped and said they were stuck here," said Buckwalter.
Rideshares became hard to come by -- some offered to share rides with stranded strangers.
"I'm going to jump in an Uber and it's gonna take me back to New York, and I had to bribe the driver with $50 of cash otherwise they weren't going to come," said Zohaiv Rathore of New York City.
An official in Middlesex County said the fires there were caused from sparks emitted by a freight train:
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"Middlesex County Department of Public Safety & Health has identified brush fires in several towns in the County resulting from sparks emitted by a freight train. Currently, the Northeast Corridor line of NJ Transit has been shut down from Metuchen station to New Brunswick station. There are ongoing efforts by local fire departments to contain the fires."
Officials reported three brush fires in Middlesex County including in New Brunswick at Rutgers Gardens, Edison and Highland Park.
Big flames could also be seen at a fourth location in Matawan, where the fire spread to a nearby abandoned train trestle.
New Jersey Transit rail tickets and passes will continue to be cross-honored by PATH at Newark Penn Station and 33rd Street.
Amtrak has since resumed service between New York Penn Station and Philadelphia.
Amtrak customers can follow @AmtrakNECAlerts on Twitter for updates.