Approximately 1,200 commuters were affected, New York City's Office of Emergency Management reported.
Reported delays of up to 45 minutes continued until 5 o'clock.
A team had to assess the damage before the train eventually made its way to Penn Station, according to NYC Fire Wire.
NJ Transit's Northeast Corridor train #3850 left Trenton at 1:44 p.m. and was scheduled to arrive at New York's Penn Station at 3:15.
All trains in the river tunnels were affected by power problems after it became disabled, authorities said.
City firefighters went to Penn Station to help any passengers who needed it.
Amtak issued a statement:
"Amtrak engineering forces are assisting a NJ Transit train that became disabled in the south tube of the Hudson Tunnel. Crews will need to inspect the train before moving it. Customers should expect delays between New York and Newark, NJ until the train is moved."
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