American Airlines Flight #4464 originated in Indianapolis, Indiana with the call sign, "Brickyard" and veered into the path of Air Canada Flight #554, which originated in in Toronto, Canada with the call sign "Jazz 554."
The close call happened around 2:30 p.m.
In the air traffic control audio, anti-collision alarms are heard blaring in the tower and cockpit.
Controllers told pilots in both planes to take evasive actions and both jets aborted their landings. The pilots told the controllers they were responding to the RA alarm, which is the most serious of the anti-collision warnings pilots can get.
The two planes came within 350 feet vertically and .62 miles horizontally at their closest points, according to FlightRadar24.
Both planes went around and landed without incident.
The FAA released a statement and said it was investigating:
"The crew of Republic Airways Flight 4464 performed a go-around at John F. Kennedy International Airport after missing the intended approach path and flying too close to Jazz Aviation Flight 554, which was cleared to land on a parallel runway. Both flight crews responded to onboard alerts."
The near collision comes after a deadly crash at LaGuardia Airport last month. That crash also involved a Jazz Aviation flight operating on behalf of Air Canada.
The plane crashed into a truck after it requested permission to cross the runway and two pilots on the plane were killed.
(ABC News contributed to this report.)
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