The spokesperson later said that an "all clear" was given after an NYPD bomb squad investigation, and that the package had been a "toothpaste tube with tape around it".
Passengers and employees have returned to the terminal.
WABC-TV had earlier reported that a source had told them a "suspicious package was being boarded on to a plane" around 4.10pm EDT. According to NBC New York, the package was found "discovered in the bag room of El Al Airlines."