Twenty-four-year-old Siyah Bryant of Jersey City was charged with trespassing around 4:45 a.m. Wednesday.
Port Authority of New York and New Jersey Police Chief Louie Koumoutsos said in a statement Thursday that the airport's perimeter security system worked and that an alarm was raised after cameras showed Bryant going over the fence.
Koumoutsos said he wants to find out why it took "an unacceptably long time" for officers to find Bryant.
The investigation will also focus on the third-party operator responsible for monitoring the cameras. Bryan was released with a summons. A phone number for him could not be located.