Aside from the schedule confusion and marathon transfers, there’s a much simpler reason why last month’s opening of full service to Grand Central Madison has caused problems for riders: Nearly a quarter of the Long Island Rail Road’s train cars can’t run through the East River tunnel that serves the new station.

That has limited service into the East Side Access terminal. And the MTA's failure to order new LIRR cars has forced the agency to bring some of its oldest and least reliable train cars out of retirement.

To run the new service, the MTA has been forced to operate fewer trains to and from Penn Station, which means more riders must make frustrating transfers at Jamaica Terminal.

Officials at the MTA were aware the train fleet could cause problems for the new service as far back as 2016, according to records from the Federal Transit Administration.

The tunnel used by trains going to Grand Central Madison was completed in the early 1970s, but it's too small for the LIRR’s diesel trains. The tube runs between Long Island City and East 63rd Street, carrying subway trains on its upper level and LIRR trains on the lower level.

The agency’s diesel trains, which serve areas of Long Island without electrified tracks, are 14 feet tall. And MTA officials said its M3 train cars from the 1980s are small enough to fit in the tunnel, but do not have the right equipment to run on its tracks. .

Those trains make up 22% of the LIRR's fleet, and the only East River tunnels they fit in are the ones serving Penn Station.

The MTA’s service plan for the launch of Grand Central Madison could have been more flexible had it made good on previous plans to order 160 new electric train cars, known as M9As, to run service into the new terminal.

But, like so many things at the MTA that rely on third party vendors, the order was botched.

Federal reports show the train car order was already behind schedule in late 2016.

By early 2018, they still had not been ordered. The Federal Transit Administration’s Project Management Oversight Contractor, who was monitoring the project, then called East Side Access, wrote the agency “remains concerned about the schedule slippage.”

The MTA nixed the plan to order those cars in September 2018, records show. The authority said it would increase the order from 160 to 460 train cars, splitting the order with Metro-North, and hoped to award a contract by June of 2019.

June came and went, and records show the MTA told the feds it might finalize the contract for the new rail cars by October 2019. Even at that late date, with the time it takes to manufacture and test train cars, they wouldn’t be ready to hit the tracks before April 2023, the feds noted.

The feds warned in their July 2019 monthly report on the project that the MTA will need to “determine how to supply vehicles from its existing fleet in order to begin LIRR service into GCT [Grand Central Terminal].”

Fast forward to today, and that’s exactly what’s happening.

When the new terminal opened, the MTA increased LIRR service by 41%. To do so, it had to put some of its oldest trains — the 1980s-era M3s with their wood paneling and occasionally duct-taped seats — back into service.

“The LIRR retained 100 M3 cars that had been slated for retirement in order to expand capacity for the Grand Central Madison-related service increases,” MTA spokesperson Aaron Donovan wrote in a statement.

The new M9A train cars have still not been ordered.

The MTA is also waiting on the manufacturer Kawasaki to deliver 50 out of 202 cars the agency ordered for the LIRR in 2013. The company is the only one that's built trains for the railroad since the late 2000s.

The new terminal may lure riders back to the LIRR. Last Tuesday, the railroad saw its second highest ridership since the pandemic began with 205,559 riders. That figure is still only 66% of pre-pandemic ridership and a fraction of the 3,766,431 subway riders the MTA reported the same day.

MTA officials said the LIRR receives more subsidies than any other of the agency’s properties. The agency spent $11.6 billion to build the new service into Grand Central Madison.

Roughly 40% of LIRR commuters are now heading into Grand Central Madison, MTA data shows. But looming construction efforts by Amtrak may force the MTA to send more trains into the new terminal where a sizable chunk of the LIRR’s fleet can’t fit.

Amtrak operates two East River tunnels used by the LIRR, Amtrak trains and NJ Transit trains that head to Sunnyside Yard for storage. But Amtrak needs to repair one of those tunnels, which was damaged in 2012 during Hurricane Sandy. While the tunnel is repaired, space for all those trains will be limited to one tube.

MTA officials said some tweaks to LIRR service may be necessary once the tunnel repairs are underway.

CORRECTION: This story was updated to distinguish which LIRR train cars can fit in the Grand Central Madison tunnel versus which ones are not equipped to operate in the tube.