A senior Amtrak official said Friday the agency is ready to tackle the repairs at Penn Station that will disrupt the commutes of tens of thousands of Long Island Rail Road riders this summer, and at the same time sought to allay concerns about another train derailment at the station the night before.

Scot Naparstek, chief operating officer for the national rail agency, which owns Penn Station, said that the derailment of a New Jersey Transit train as it entered Penn on Thursday night would not impact the planned infrastructure renewal work that will require taking several tracks out of service throughout the summer.

Naparstek also said Friday those track outages were set to begin that night although LIRR customers won’t notice them until the Monday morning rush hour.

The derailment, Naparstek said, occurred in the same general area, just west of Penn’s platforms, as two other derailments in the spring. He said the cause of Thursday’s derailment, which did not cause any injuries, is still under investigation.

Amtrak workers were able to remove the derailed train and repair what Naparstek said was “very minor damage” to the tracks before the morning rush hour. The LIRR told customers around 5 a.m. to expect “normal morning rush-hour service” to and from Penn Station.

Naparstek said the derailment would have “no effect” on the planned summer infrastructure renewal work, in part because the affected track was set to be taken out of service as part of the project last night anyway.

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“What it really emphasizes is why the work that we’re beginning tonight is so critical,” Naparstek said.

If other unexpected services disruptions arise while Penn Station is operating at reduced capacity, Naparstek said Amtrak will be ready. He said the agency, which is responsible for all maintenance and repairs of Penn Station, has postponed other projects on its lines in the Northeast to have extra crews on standby in Manhattan to respond to any incidents.

It was the two spring derailments, occurring within a span of 10 days, that led Amtrak to undertake the effort to replace aging track components at Penn, the nation’s busiest train station, serving about 600,000 customers daily.

The track outages are forcing the LIRR to reduce rush-hour service into and out of Penn by 20 percent. It’s running extra trains outside of the rush hours, diverting other trains to terminals in Brooklyn and Queens and also supplementing train service with the buses and ferries to help move its nearly 300,000 daily LIRR riders.

MTA officials have said they’ll keep a close eye on the construction work to make sure it progresses on schedule.

Naparstek said that while “there’s nothing definite in the world,” he remains “extremely confident” Penn Station service would be fully restored by the morning rush hour of Sept 5 — the day after Labor Day.

Naparstek said early stages of the work, which began in May, have kept on schedule. In recent days, Amtrak has prepared construction equipment and materials at a staging area near Penn, mapped out routes to bring other materials into and out of the station and gone over the plan with work crews.

“We have the resources, we have a plan and, frankly, we think we have the expertise to do this,” he said.