Union leaders said the MTA hired “scab” drivers to run the agency’s shuttle buses to carry would-be Long Island Rail Road commuters on Monday who were stranded by the labor strike that shut down the train service.

Buses run by companies including Peter Pan, Coach USA and J & F Tours picked up passengers at five LIRR stations, and dropped them off at the Jamaica-179th Street and Howard Beach-JFK subway stations in the city during the morning rush.

The shuttle buses didn’t run over the weekend, but the MTA launched the service on Monday as the strike dragged into the workweek. Agency officials said bus operation costs roughly $550,000 a day, and that around 2,100 people used the buses on Monday morning, even though they had the capacity to fit around 13,000 travelers.

Union leaders said the drivers were crossing the picket line by providing rides that replaced LIRR service.

“ Anybody that's been a union member — I'm a 50-year member — the thing is we don't like scabbing,” said Jim Louis, national vice president of the Brotherhood of Locomotive Engineers and Trainmen, as he picketed outside Penn Station.

A driver running one of the MTA's shuttle buses during the LIRR strike had a hat bearing the phrase "unity" on the dashboard while parked at Hicksville station.

MTA representatives did not respond to questions about the shuttle bus drivers.

In previous generations, New York labor unions would get into violent donnybrooks and attack scabs during labor strikes. Louis said that type of behavior would be out of the question for his union’s members.

“There's a reason it's called scab. But we understand that there's situations like this that sometimes it comes to that,” Louis said. “The last thing we want to do is have any violence out here. We just want to get our contract.”

Many of the relatively small group of riders who relied on the shuttle buses were grateful that the MTA provided the service.

“The bus actually wasn’t that bad,” said 53-year-old Henry Manzano, who got off the bus from Long Island and works at a fashion company where he needs to be in person. “These drivers were good and everything. They did their job. But it really puts a stranglehold on all of us. It really hurts the commuter more than anything else.”

John Samuelsen, international president of the Transport Workers Union, said the MTA tried to give a contract to Shortline Bus to run shuttle buses during the strike. He said they declined because the company's drivers are represented by TWU Local 225, which is standing in solidarity with the striking LIRR unions.

“It is scabbing and we refused to do it,” Samuelsen said. “Our local offices refused without me having to intervene.”

Coach USA spokesperson Dan Rodriguez defended the company's contract with the MTA.

He said the company wants "to assure that essential workers such as nurses, firemen and those working throughout the metropolitan area who cannot work from home and who many depend on, are able to do so with as little as possible interruption."

Representatives for Peter Pan and J & F Tours either did not respond to requests for comment or declined to do so.

The unions on strike said that negotiations with the MTA began again on Monday morning. A source familiar with the negotiations described the discussion as going very slowly.

Stephen Nessen contributed reporting to this story.