The MTA’s delay-plagued East Side Access megaproject is falling further behind schedule, largely because Amtrak continues to deny workers the access they need at a critical construction site, project officials said.

The $10.2 billion effort to link the Long Island Rail Road to Grand Central Terminal via newly-bored tunnels has already had its completion date pushed back by 13 years since it was first proposed in the late 1990s.

Last week, at a meeting of the Metropolitan Transportation Authority’s Capital Program Oversight Committee, project executive Bill Goodrich revealed that since February construction delays at the busy Harold Interlocking in Long Island City have been “getting worse.”

The LIRR shares use of the busy rail junction with Amtrak. To carry out work there, East Side Access construction crews rely heavily on Amtrak taking some tracks out of service on specified nights and weekends, and lending some of its workers to the effort.

But despite written agreements with Amtrak detailing their expected cooperation, Goodrich said project workers “have not been receiving the level of support” from Amtrak that the agency has promised.

“The end result is when something gets scheduled on a weekend or weeknight . . . it gets canceled, because the resources aren’t available,” said Goodrich, adding that the lack of help from Amtrak has caused key mining efforts at Harold to fall another two weeks behind schedule in just the last three months.

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The repeated delays have contributed to major cost over runs. East Side Access was originally projected to cost $4.3 billion, or less than half the current estimate of $10.2 billion.

Project planners have built in a 22-month “contingency” that allows for some delays while still meeting the goal of running trains to Grand Central by December 2022. But project officials say that risks, like those posed by the Amtrak access problems, threaten to eat away at that cushion.

MTA spokesman Aaron Donovan said that of 10 “priority weekends” promised by Amtrak this year for East Side Access, five have been granted, and none are scheduled for the remainder of the year.

Amtrak spokesman Craig Schulz said the agency “has increased its level of support for East Side Access to help advance the project,” but added that the MTA’s schedule for the project assumes track outages “that go beyond our existing commitments.”

“While the schedule hinges on a number of variables beyond Amtrak’s support, we continue to work closely with MTA to coordinate scheduling and minimize any potential disruption,” Schulz said.

MTA and Amtrak officials have said other construction projects in and around Penn Station, including repairs to the East River tunnels, the Moynihan Station project at the Farley Post Office building, and Amtrak’s Gateway proposal for a new Hudson River tunnel, have competed for Amtrak’s time and resources.

MTA officials have been raising concerns about Amtrak’s level of cooperation since last year. In October, Goodrich reported that project workers had been denied the access they needed from Amtrak on 14 out of the 19 previous weekends. At the time, Amtrak said it would work with its “valued partners . . . to satisfy all these important needs.”

“We’ve never been able to get critical mass — them giving us the resources we need,” said MTA Chairman Thomas Prendergast, adding that the authority will “crank . . . up a couple of notches” its pressure on Amtrak to cooperate. “I think we need to put it on their radar screens that we need to actually have it stepped up.”

But without the leverage needed to get Amtrak to comply, MTA Board member Mitchell Pally isn’t optimistic about the situation improving.

“We’ve been through this over and over and over and we get further and further behind,” he said. “From their perspective, it’s not a high priority. From our perspective, it’s the highest priority.”