A major disruption on the Long Island Rail Road Wednesday morning has reignited a dispute between the MTA and Amtrak over how to carry out upcoming tunnel repairs beneath the East River.

Commuters faced widespread delays and cancellations after Amtrak temporarily shut down one of the four tunnels leading into Penn Station. The outage resulted in five train cancellations and 43 delays, prompting MTA officials to warn that plans for future tunnel closures could lead to even greater service breakdowns.

“This is what we warned people about and we’re not happy about it,” said LIRR President Rob Free. “Sixty-two a.m. peak trains in and out of here is not sustainable with one tunnel. There would have been a shutdown if line two had been out of service — and that’s what we’re trying to explain.”

Amtrak, which owns and maintains the East River tunnels, is planning a full closure of one tunnel later this month for long-term repair work. Another tunnel is reserved exclusively for Amtrak and New Jersey Transit. That would leave just two tunnels available for LIRR trains to travel to and from Manhattan, a scenario the MTA says is unworkable.

The MTA has proposed a less disruptive alternative: limiting repair work to nights and weekends. But Amtrak officials argue that a full tunnel closure is ultimately more efficient and less prone to surprise outages like the one seen Wednesday.

“Unexpected service disruptions, like the one experienced today, are far worse than a well-coordinated and well-planned approach that are scheduled in advance and have stronger mitigation plans in place,” Amtrak said in a statement.

Franny Bavaro, a commuter from Sayville, echoed concerns shared by many riders: “I think they should consider overnight and weekend work — not impact people who have to go to work every day.”

The long-term repair project was initially set to begin this week but has been delayed until May 23. In response to mounting concerns, Amtrak’s president has requested a meeting with Gov. Kathy Hochul and MTA leaders to discuss a path forward.