The Transportation Security Administration says an airline greeter rushed them past a security checkpoint at John F. Kennedy Airport so they could catch their flight to Los Angeles.
But authorities say the couple was supposed to be privately screened.
ABC News says when the breach was detected, Kardashian and West were reportedly yanked off the plane.
TSA agents then made them go through security, delaying the flight by about an hour. They were eventually cleared.
Kardashian, 32, and West, 35, were photographed in Rio de Janeiro over the weekend visiting the Christ the Redeemer statue.
Kardashian didn't mention the security breach on her Twitter account Wednesday, but she did say she was glad to be back in Los Angeles to start filming the eighth season of "Keeping up with the Kardashians."
The rapper and reality TV star announced late last year that they are expecting their first baby.
ABC News and the Associated Press contributed to this report.