The Metropolitan Transportation Authority will reduce fares for some LIRR customers impacted by service disruptions from this summer’s Penn Station track repairs, according to the MTA chief, who vowed Monday to withhold funding from Amtrak and make it pay costs incurred by the Long Island Rail Road.

MTA interim Executive Director Veronique Hakim’s announcement — a reversal from the authority’s position a week ago — came after Gov. Andrew M. Cuomo earlier Monday urged the LIRR to reduce fares for riders during July and August. A planned Amtrak infrastructure renewal project at Penn Station will reduce the railroad’s capacity to run rush-hour trains to and from the Manhattan terminal, and result in some trains being diverted to other stations.

“I think the Long Island Rail Road should consider reducing the fares on those diverted trains,’’ Cuomo said. ‘‘That’s only fair to the people who are taking those trains. And you want to make sure people do take those diverted trains.”

“If [they] bought a ticket from Long Island to Penn and they’re not getting into Penn, then I believe they should have a reduced fare,” the governor said at a ceremony marking the formal opening of the new customer concourse at the west end of Penn Station, under the Farley Post Office building on Eighth Avenue.

Cuomo’s call received immediate praise from Democratic and Republican state lawmakers and from the railroad’s official watchdog group, the LIRR Commuter Council. Its chairman, Mark Epstein, said it is “only fair that riders who are receiving reduced service are charged a reduced fare for their travel.”

Hakim, in a statement Monday, said Cuomo “is right that due to Amtrak’s repairs some customers are paying for a service they won’t be getting this summer — and that they deserve a fare decrease.”

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“We intend to follow the Governor’s lead and make sure our riders are fairly compensated,” Hakim said.

The statement was a switch from last week, when Hakim said that, rather than giving riders a break on their fares during the summer outages, the MTA was focusing on giving them transportation options, including by adding trains outside of the rush hours, lengthening rush-hour trains with additional cars, and supplementing train service with express buses and ferries.

MTA Board member Mitchell Pally said he expects the 17-member panel to hash out the specifics of a potential fare cut at a Manhattan meeting Wednesday, including whether it would be given to all customers or only to those on trains diverted from Penn. The railroad has 88,000 daily commuters who travel to and from Penn, the nation’s busiest rail station.

Pally, of Stony Brook, said he’ll be recommending a reduction of 15 percent — “a reasonable number” that the MTA can afford, regardless of whether it recoups its money from Amtrak. The cost of a monthly LIRR ticket to and from Penn Station ranges from $190 to $500.

“You have to do something meaningful,” Pally said. “I don’t want to have to rely on them being good to us for us to be good to our customers. We should do that no matter what.”

In a statement, Sen. Elaine Phillips (R-Manhasset), who first proposed a fare cut for riders this summer, said she was encouraged by Cuomo’s call. “If service is being cut, fares should be cut too,” she said.

Sen. Todd Kaminsky (D-Long Beach) also said the potential fare cut is welcome news to LIRR commuters. “Any monies directed toward commuters goes a long way in giving them back the respect and dignity that’s been absent lately,” he said.

Earlier Monday, Hakim made a rare appearance at the regular monthly meeting of the MTA Board’s LIRR Committee to make it clear neither the MTA nor its riders would be footing the bill for the LIRR’s summer service plan.

“I wanted to affirmatively let the board know that our intent is to withhold any further payments to Amtrak,’’ Hakim said. “We fully intend to have them pay those costs to the MTA.”

In a statement Monday, Amtrak spokesman Mike Tolbert said the MTA “has no basis to require Amtrak to pay for the cost of reductions in its fares” and “shouldn’t presume that Amtrak will pay for these or any other costs while we do the major renewal work at Penn Station.”

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“This rehabilitation work benefits all users at Penn Station” Amtrak said. The railroad has not provided an estimate for its planned summer infrastructure renewal work, which it says has already been funded.

Hakim’s announcement follows another call last week from Cuomo for the MTA to hold back its annual payments to Amtrak, which total about $46 million in capital and operating contributions and rent for its space at Penn Station.

Hakim’s vow was praised by some board members, who criticized Amtrak’s neglect of the 110-year-old train terminal that has been beset by infrastructure failures and resulting service disruptions in recent months.

Others, however, questioned the logic of withholding Amtrak funding. Board member Veronica Vanterpool said many issues at Penn Station are the result of decades of financial neglect by the federal government. Further starving Amtrak of funds appeared “hasty” and a “knee-jerk reaction,” she said.

“Is that a rational response to a problem that we may not have all the answers to?” Vanterpool asked. “This is a problem of funding. And I think Amtrak has been a victim of 46 years of inadequate funding.”

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Some board members urged the MTA to push for increased federal dollars to address the Penn Station commuting crisis — even echoing a call from Cuomo last month in a letter to President Donald Trump to have the situation declared a federal emergency.

With Laura Figueroa