2:00 PM PT -- A rep for American Airlines tells TMZ ... the company is taking responsibility for the incident, explaining, "This was a lapse in judgment by one of our employees."
AA adds, "We’re working closely with the TSA and speaking to the individuals involved to better understand what happened."
But the airline says the 50-minute delay wasn't ENTIRELY due to the Kimye incident ... saying, "It was delayed in part ... because a number of connecting bags were delayed getting to the aircraft."
Kim Kardashian and Kanye West are at the center of a TSA investigation following a major security violation at JFK yesterday ... but the TSA tells TMZ Kimye is NOT to blame.
We've learned ... K&K had taken a flight from Brazil to JFK on Tuesday, where the plan was to catch a connecting flight to Los Angeles.
But once they landed in NY, the couple met up with an airline greeter ... who, according to the TSA, allowed them to bypass a key security checkpoint to get them to their next flight as quickly as possible.
After Kim and Kanye took their seats on the L.A.-bound plane ... a TSA agent yanked them off the flight ... and made K&K go through another layer of security.
We're told the plane was delayed for roughly an hour while the couple was screened by TSA agents.
Now, the TSA tells us it wasn't Kim and Kanye's fault ...explaining, "An airline employee escorted the two travelers through a non-public area in order to provide expedited access to their domestic flight."
"In doing so, the airline employee violated security protocols by permitting the travelers to by-pass the TSA security checkpoint. TSA officials learned of the violation and conducted a private screening of the two passengers in the area of the jetway."
"The passengers were cleared to board their flight, which departed after a delay of approximately 50 minutes. TSA is actively investigating the incident."
The couple ultimately touched down in L.A. ... where they were greeted by a gaggle of paparazzi ... but seemed incredibly calm considering all they had been through.