The MTA suspended two supervisors Wednesday who oversaw work on the track where an A train derailed a day earlier.
"They have been suspended without pay pending a formal review process," said MTA spokesman Kevin Ortiz.
The derailment in Harlem injuring 34 people and sparking major delays is being blamed on human error and not a track defect.
A preliminary investigation indicates the derailment just before 10 a.m. Tuesday near the 125th Street Station was caused by "an improperly secured piece of replacement rail that was stored on the tracks," Metropolitan Transportation Authority Chairman Joe Lhota and Interim Executive Director Ronnie Hakim said in a joint statement late Tuesday night.
"Storing equipment in between tracks is a common practice employed by railroads across the country to accelerate rail repairs," the statement said. "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 emergency brake was activated between 9:30 a.m. and 10 a.m. The derailment tossed people to the floor and forced hundreds of passengers to evacuate through darkened tunnels.
Crews are inspecting "every inch of rail" to ensure that every replacement part "is properly stored and secured," MTA officials said, adding that the investigation is ongoing.
MTA officials said crews still were repairing tracks damaged in the derailment Wednesday morning. The agency was hoping to restore normal service for morning commuters. Just before 9 a.m., the MTA announced service had resumed on the A, B, C and D lines with delays. A and D express service also resumed with delays.
The Associated Press contributed to this report.