As the MTA seeks a rescue from Albany, its leader acknowledged Wednesday that outdated staffing practices and decades-old work rules at the Long Island Rail Road are costing commuters and straphangers millions.

“Do we have, on our operating side, a ways to go to make sure that maybe antiquated rules, work rules and ways of working do not cause the MTA to spend more money than the first-class modern transit systems we look at as our peers?” Janno Lieber told WNYC radio. “Sure, we have a ways to go.”

A seven-month Post investigation revealed last month that the MTA could save at least $200 million annually by operating the LIRR as efficiently as its other major railroad, Metro-North.

“A lot of that stuff is at the collective bargaining table, though,” Lieber said. “So, you can’t just change overnight the number of people that are assigned to a particular task, even if those assignment patterns date from, you know, 50, 60, 100 years ago, which some of them do.

“We have to win those changes at the bargaining table with our union.”

The last time the MTA pushed hard for LIRR work rule changes was in 1994 and it triggered a strike.

Then-Gov. Mario Cuomo quickly backed down and agreed to a settlement, which his furious MTA chairman Peter Stangl described at the time as a ransom.

Lieber’s remarks built upon what he told state lawmakers during a budget hearing earlier this month when he said the MTA would “put those issues on the table.”

The Post investigation revealed that the dramatic costs and inefficiencies at the LIRR mean commuters pay some of the highest fares in the country — but are still forced to contend with longer waits and more crowded trains.

It also found the LIRR has double the conductors and assistant conductors it needs to both meet minimum contractual obligations and run its full peak schedule from before the COVID-19 pandemic, which alone costs $130 million annually.

Additionally, generous contracts mean that engineers can earn quadruple pay for standard shifts, while conductors can earn double pay by working a special train to Citi Field when the Mets play a home game.

Lieber’s comments come as opposition grows to two of Gov. Kathy Hochul’s biggest proposals to shore up the MTA’s finances, which would net the agency at least $1.3 billion annually.

The biggest chunk — $800 million — would come from raising the MTA’s downstate payroll tax from .34% to .50%. That pitch is facing opposition from at least three suburban lawmakers who only want the hike applied to the five boroughs.

Meanwhile, City Hall is pushing back hard against the gov’s request to have the city pick up $500 million in expenses incurred by the MTA to provide the Big Apple’s paratransit service and student Metrocards.

As part of Hochul’s plan, Lieber has promised to find $400 million in annual savings, though the agency has yet to release a detail accounting of how it plans to do so.