The MTA on Wednesday suspended two supervisors without pay over the Harlem subway derailment that injured dozens of riders — but union chiefs pointed the finger at the agency’s safety protocols.

About 12 hours before a southbound A train jumped the tracks as it was approaching the 125th Street-St. Nicholas Avenue station, the supervisors had been overseeing work on a defective rail.

When the job was done, track workers stored a 13-foot, 430-pound piece of spare rail in the track-bed trough, a piece that the MTA said wasn’t secured.

At about 9:50 a.m. Tuesday, the undercarriage of an A-train car somehow came in contact with the loose piece of rail, jolting the train, setting off the emergency brake and causing two cars to derail. In the chaos, 39 people were injured.

The Federal Railroad Administration has opened an investigation, sources said Wednesday.

“The two supervisors who were responsible for oversight of the work have been suspended without pay pending a formal review process,” said MTA spokeswoman Beth DeFalco.

“There are proper protocols to ensure equipment is fastened and cannot shake loose and that equipment that is too small to be safely stored is never stored in between tracks,” she added.

Sources said a rail piece shorter than 19¹/₂ feet is not supposed to be left in the trough.

“[Track workers] should have taken it with them,” said one source.

But another source said, “What is the supervisor supposed to do, pick it up and carry it out over his shoulder? The only way to get rid of a length of rail is to call in a work train, and he doesn’t have the authority to do that.”

Mike Carrube, president of the Subway Surface Supervisors Association, said the bosses shouldn’t be blamed.

He said the MTA should have long ago changed its practice of having workers leave unused rail pieces for a work train to pick up.

“Just because nothing happened all these years doesn’t mean that it couldn’t happen,” Carrube said.

Transport Workers Union Local 100 President John Samuelsen also disputed the MTA’s claim that ultimately “human error” caused the derailment.

“A properly secured rail vibrates and it has the ability to catch onto something,” he said.

“The edge of the rail could dig into the side of a tie or a plate or it could pivot into the underbelly of a train. It doesn’t mean it’s human error, and it’s not a provable conclusion to say it wasn’t properly secured.”