Olajide Oluwaseun Noibi cleared security last Friday to board Virgin America Flight 415 and travel to Los Angeles International Airport, FOX News Channel reported Thursday.
The Transportation Security Administration (TSA) confirmed Noibi was screened at JFK, but said it could not comment further due to the ongoing FBI investigation.
"Every passenger that passes through security checkpoints is subject to many layers of security including thorough physical screening at the checkpoint. TSA's review of this matter indicates that the passenger went through screening," spokesman Greg Soule said in a statement. "It is important to note that this passenger was subject to the same physical screening at the checkpoint as other passengers."
Noibi apparently stayed in Los Angeles before returning to the airport Wednesday and attempting to board a Delta flight bound for Atlanta using the same means.
He was prevented from getting on the flight and taken into custody after investigators found that he was in possession of several expired boarding passes.
FBI special agent Kevin Hogg said in an affidavit that the man whose name was on the expired boarding pass, used by Noibi on the Virgin America flight, told him it disappeared from his back pocket on a subway ride to the airport last Thursday.
Hogg said that Noibi acknowledged that he did not pay for the Virgin America flight and told officials that the reason for his trip to Los Angeles "was to recruit people for his software business."
He was charged with being a stowaway aboard an aircraft, a felony punishable with up to five years in prison if convicted.
According to officials first cited by KABC, Virgin America's flight crew only realized that an extra passenger was on board after the flight was airborne.