New Jersey Transit spokesman Dan Stessel says the train was headed for New York when the locomotive broke down near the Portal Bridge in Secaucus around 7 a.m. Monday.
Stessel says passengers couldn't be safely transferred to another train and there was difficulty towing the disabled train.
It was pulled into New York's Penn Station at 8:45 a.m.
NJ Transit trains on the Northeast Corridor, North Jersey Coast Line and Midtown Direct operated up to 60 minutes behind schedule in and out of New York City until about 11:30 a.m.
Amtrak trains were back on schedule after morning delays.
The incident came just days after damaged wires suspended rail service in the same area on Wednesday.
Meanwhile, the railroad also had to fix switch problems in Summit that caused trouble earlier.
There were delays of up to 30 minutes in both directions on the Morris and Essex Line, including Midtown Direct service early Monday.