Air traffic controllers immediately alerted pilots on the Delta flight 1943 of the incoming aircraft and pilots were able to slam on the brakes with only about 300 metres to spare, according to the FAA.
ATC audio reveals the American Airlines aircraft did not follow the correct instructions.
Aviation expert Ross Feinstein shared the audio clip to Twitter, in which ATC can be heard instructing the plane to “cross runway 31 Left and Kilo”. Instead, the American Airlines flight crossed runway 4 Left at Juliet, which the Delta flight was departing from.
More of the audio is now available via @liveatc. @FAANews@JFKairport to American 106: "Cross Runway 31L at Kilo."
The American Airlines flight was still able to depart to London with only a 30-minute delay according to data from Flight Aware. Unfortunately for those heading to Santo Domingo, their Delta flight was delayed until the following morning.
An overnight delay could have been for a number of reasons, such as giving maintenance time to check the aircraft after the use of heavy brakes, crew timing out or giving pilots time to shake off the scare.
Delta apologised to customers and said the incident was being investigated.
“Delta will work with and assist aviation authorities on a full review of flight 1943 on Jan. 13 regarding an aborted takeoff procedure at New York-JFK. We apologize to our customers for the inconvenience and delay of their travels,” the airline said in a statement.
American Airlines reportedly deferred to the FAA when approached for comment.
