Amtrak infrastructure repairs at Penn Station are causing the MTA’s East Side Access project — plagued by years of delays and cost overruns — to fall further behind and miss key milestones that were supposed to be met this summer.

Amtrak’s infrastructure renewal work at Penn has resulted in East Side Access crews “in effect standing down” on planned work because of Amtrak’s inability to provide needed assistance in the form of employees at the busy Harold Interlocking in Queens, where the railroad also operates, said East Side Access project executive Bill Goodrich.

When the Metropolitan Transportation Authority last adjusted its schedule for the $10.2 billion East Side Access project, which officials estimate will be completed by late 2022, it built in a two-year “contingency” cushion to account for possible delays. However, MTA board member Ira Greenberg, who represents the LIRR Commuter Council, said Monday at a meeting of the MTA’s Long Island Rail Road Committee that recent delays could mean “losing almost all our contingency.”

“The problems that we’ve had with Amtrak aren’t just related to this small summer thing. We’ve had ongoing issues with Amtrak,” said Greenberg, noting that the very work that is getting in the way of East Side Access speaks to the importance of giving riders an alternative to Penn Station. “If East Side Access had opened on time . . . this summer would not be the ‘summer of hell.’ ”

The latest setback for East Side Access comes as frequent breakdowns on deteriorating regional transportation systems — including the LIRR and New York City subways — are increasingly frustrating riders.

Commuter disruptions blamed on Penn Station’s infrastructure include two derailments in 10 days this spring at the nation’s busiest rail hub, owned and operated by Amtrak. The incidents spurred the railroad to shut down three of its 21 tracks for repairs during what Gov. Andrew M. Cuomo has dubbed the ‘‘summer of hell.’’

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Proponents say East Side Access would be transformational for the LIRR, cutting the commutes of 162,000 projected daily riders by 20 minutes each way and raising property values throughout Long Island by providing a direct link to Manhattan’s East Side. Considered the largest public works project underway in the nation, East Side Access, along with the MTA’s double track and third track projects on Long Island, is vital to rebuilding the region’s public transportation system, proponents say.

Since 2015, MTA officials have complained about the lack of cooperation from Amtrak, which has said its resources have been stretched thin by other projects in the area.

Goodrich said 13 Amtrak track foremen would be needed to carry out the scheduled workload at Harold Interlocking. Amtrak had been providing nine foremen, but reduced that number to four for the duration of the summer work, which is expected to last until about Labor Day, Goodrich said.

Because of the lack of support from Amtrak, some key milestones expected to be reached in July and August, including “pretesting” for new signals on the East Side Access tracks, will have to be pushed back to September and October, Goodrich said.

“It does have an impact,” he said, adding that the MTA is evaluating the effect of the delays on the project’s budget and timeline.

East Side Access has been plagued by delays and cost overruns since it was proposed in the 1990s with a budget of $4.3 billion and a targeted completion date of 2009. That cost estimate has more than doubled and the target completion date has been pushed back 13 years.

Despite the latest hiccup for East Side Access, MTA officials Monday otherwise celebrated how smoothly the Penn Station service disruptions have gone so far.

LIRR president Patrick Nowakowski, making his first public comments since the track shutdowns began two weeks ago, commended MTA planners, LIRR laborers and customers all for doing their part in ensuring that the agency’s effort to make do with three fewer tracks at Penn Station has been “successful.”

“This was an all-hands-on-deck exercise,” Nowakowski said. “I would characterize it as one that has very much gone according to plan.”

Nowakowski said that, compared with ridership counts taken in June, the number of people traveling into Penn Station in the mornings dropped by about 10,000 people — from about 86,000 to about 76,000. Meanwhile, ridership at Atlantic Terminal increased about 50 percent. At Hunterspoint Avenue in Queens, it nearly doubled to about 6,000.

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“We are seeing that shift that we needed,” Nowakowski said. “People did change their commuting patterns. To some extent, it was forced, because there was less service.”