Long Islanders should still expect delays and cancellations for their Friday morning commute after service in and out of Penn Station was shut down earlier this morning.

Around 5 a.m., the Metropolitan Transportation Authority announced service was restored, but warned issues will likely still persist as the agency works to get back on track.

The issue stemmed from fire department activity involving an Amtrak work engine at Penn Station.

An Amtrak spokesperson said there was a smoke and fire condition involving an Amtrak contractor maintenance vehicle in the Hudson River tunnels just before 1:30 a.m. The fire shut down all rail service between New York and New Jersey.

"Amtrak apologizes for the inconvenience and is providing rebooking opportunities and refunds while it works to return to scheduled service levels," a spokesperson told News 12.

This is the second time in two weeks that an Amtrak-related fire has completely shut down service in and out of Penn Station.

On May 14, a fire in one of the East River Tunnels caused major disruptions for commuters.

The MTA is encouraging riders to check their TrainTime app for the latest schedules.