The incident was reported just after 9 a.m. on Saturday.
The southbound train lost a wheel and came off the tracks near West 81st Street.
No one was hurt.
Dozens of passengers were transferred to another train that backed up to rescue them, and took them to Columbus Circle.
Subway service on the A, C and D lines returned to normal Sunday morning.
The MTA says it's looking into whether a broken rail caused the train to come off the tracks.
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