NEW YORK — Thousands of New Yorkers began a chaotic commute to work Monday as 11th-hour talks between the MTA and Long Island Rail Road workers failed to result in a contract.

The MTA and a consortium of unions sat at the bargaining table until about 1 a.m. Monday, but left without ending the strike, which has now gone into its third day.

With the LIRR trains shut down, commuters coming into Manhattan from Long Island were put on shuttle buses beginning at about 4:30 a.m.

Speaking to NBC’s Today in New York, MTA Chairman and CEO Janno Lieber said the turnout for the shuttle buses was pretty light, but admitted that rush hour wasn’t in full swing.

It appears that most commuters, Lieber said, took Gov. Kathy Hochul’s advice to work from home, he said.

The shuttle buses will be taking Long Islanders to several transportation hubs in Queens so travelers can take New York City Transit the rest of the way to work, he said.

City subway trains, particularly at these transportation hubs were at “are at capacity and running well today,” Lieber noted.

The MTA warned Monday that shuttle bus service was limited and could only take about 13,000 commuters to the city Monday — a small fraction of the 300,000 that use the LIRR on workdays.

“Let’s face the facts — it’s impossible to fully replace LIRR service, so effective Monday, I’m asking that regular commuters who can work from home, should. Please do so,” Hochul said Sunday.

While the MTA and LIRR workers failed to reach a contract as of 1 a.m., both parties are expected to resume talks today.

Lieber called the Sunday night session “productive” and hoped to get the contract “over the finish line” Monday, he said.

In a statement Sunday, though, two of the unions representing the workers, the IAM Union and the Transportation Communications Union, described what they called “a disconnect between Mr. Lieber and the reality faced by workers who have gone four years without a raise.”

The unions added: “There appears to be a serious communication breakdown between Janno Lieber, MTA executives and the governor’s office about the realities of these negotiations.”

The service shutdown comes after more than two years of contract negotiations, two federal mediation boards and two weeks of talks that failed to find common ground on the one outstanding issue — raises.

The two sides settled over back pay, with a handshake agreement to retroactively raise wages by 3% for 2023, 3% for 2024, and 3.5% for 2025.

The consortium of five LIRR trade unions — made up of the Brotherhood of Locomotive Engineers and Trainmen, the International Brotherhood of Electrical Workers, the Brotherhood of Railroad Signalmen, the International Association of Machinists and Aerospace Workers, and the Transportation Communications Union — demanded a 5% raise for 2026, which they said was necessary to keep up with inflation.

After initially refusing to go above 3% without further concessions on overtime work rules, MTA leadership ultimately offered 3% plus a lump-sum payment for the difference between a 3% raise and one year of pay at 4.5%.

The unions argued that such a lump sum would only cover one year, regardless of how long a future contract took to negotiate.

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