Two MTA track maintenance supervisors have been suspended without pay following the derailment of an A train in Harlem that injured 39 people Tuesday morning, according to sources.

The workers were pulled from the overnight shifts after the MTA announced that the derailment at the 125th Street station was caused by human error — an improperly secured replacement rail that was being stored on the tracks, MTA Chairman Joe Lhota and acting executive director, Ronnie Hakim, said.

“Storing equipment in between tracks is a common practice employed by railroads across the country to accelerate rail repairs,” Lhota and Hakim said in a joint statement late Tuesday. “The key to this being an effective and safe practice is making sure that the extra equipment is properly bolted down, which does not appear to have happened in this case.”

The train derailed at around 9:45 a.m. as it ran on a rail that had been replaced only hours before on Monday night, according to Paul Navarro, chairman of the track division at TWU Local 100, the union representing MTA workers.

Navarro, a 24-year vet at the MTA, said equipment has long been stored on the tracks as a “cost-cutting” measure for the agency. He said securing scrap rail onto the track is a fairly simple process.

“It takes about five minutes,” Navarro said, who visited the scene of the derailment on Tuesday. “It’s just temporary until a work train can come with a crew pick it up. A lot of time there’s no work train available, so you secure the rail until its available.”

The derailment incited chaos along the Eighth Avenue line for hundreds of commuters and hobbled service across the city. It brought extensive damage to signal, track and switch infrastructure and sparked a small track fire, MTA and union officials said.

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About 500 people stuck in stalled trains near the derailment exited their cars and leapt onto the tracks, risking their lives trying to escape. The fire and police department conducted a large-scale effort to round up those riders wandering the tracks between the 135th and 110th Street stations, according to FDNY Commissioner Daniel Nigro.

The MTA’s announcement ended speculation as to whether faulty equipment or the activation of the emergency brake had caused the derailment, the latest high-profile service failure from the state-run MTA. Earlier this month, riders were stranded for 45 minutes in a dark, sweltering F train under Manhattan, where they were left to pry at subway doors just to get a whiff of fresh air.

Advocates and elected officials on Tuesday swiftly demanded more from Gov. Andrew M. Cuomo — in terms of funding to deliver needed infrastructure repairs and a plan to improve service, which has steadily declined in recent years.

But unlike the latest service outages, usually triggered by signal problems or other infrastructure issues, Tuesday’s derailment was caused by an apparent lapse in safety protocol. The MTA assured that it would be checking all stored equipment on its tracks.

“NYCT [New York City Transit] is inspecting every inch of rail to ensure that each and every replacement part is properly stored and secured. Nothing is more important than the safety of our customers,” Lhota and Hakim said. “The investigation into this incident continues.”