Port Authority police surrounded the Los Angeles-bound JetBlue flight around 8:00 p.m. when it apparently experienced a radio issue that impacted the crew's ability to communicate.
JetBlue said the false alarm was sent to JFK tower during the radio issue which prompted a strong police response.
Port Authority Police Superintendent Edward Cetnar discussed the plane scare on Wednesday and said it was the pilot's mistake.
"He entered the wrong code which enters the hijack duress signal, obviously we have protocols in place when something like that happens we exhaust all options, communications and stuff like that," Cetnar said. "They were having communications problems, pilot was unable to communicate with the tower, and we had to make sure even though we communicated with them by phone at one point, that everything was OK."
Cetnar said they still had to make sure that the passengers were OK and there was no nefarious activity going on in the plane.
Port Authority officials said responding officers did a good job and were able to get the plane back to the gate and JetBlue took it from there.
"It was a really successful and peaceful scare, if I could put it that way," Cetnar said. "Cops did a great job last night."
Video from the runway showed dozens of emergency vehicles surrounding the plane.
#BREAKING New video shows cops entering the #Jetblue plane at #JFK. According to its tail number, appears to be flight 1623 to #LAX, departed gate just before 7:30 but never left ground. #B61623 #abc7ny #PAPD #JFK pic.twitter.com/R7w4sf2XYb— Josh Einiger (@JoshEiniger7) June 27, 2018
Scared passengers tweeted from inside the aircraft:
The FAA said it will investigate the incident.
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