Port Authority police surrounded the JetBlue flight around 8 p.m. when it apparently experienced a radio issue that impacted the crew's ability to communicate.
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JetBlue confirmed a false alarm was sent to JFK tower during the radio issue which prompted a strong police response. Passengers say heavily armed police boarded the plane to investigate.
"There was a false alarm sent to tower as a result of a radio communications failure. Aircraft was inspected and cleared with no security threat," a Port Authority spokesperson said in a statement.
Video from the runway showed dozens of emergency vehicles surrounding the plane.
Scared passengers tweeted from inside the aircraft:
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"While communication was reestablished via alternate channels, authorities responded in an abundance of caution. The aircraft was cleared and returned to the gate for inspection," a JetBlue official said in a statement.
After several hours, another plane was able to take the travelers to Los Angeles. They landed at Los Angeles International Airport at 2:30 a.m. Wednesday.
"It was really frightening. I was sitting at the window, and I counted 20 emergency vehicles, red lights, blue lights, it was really scary," said Janice Goldberg of Yorba Linda.
The FAA said it will investigate the incident.