Hogan said security footage showed the 9-year-old "waited until the person who was at the gate was busy, and that's when he got on the plane."
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The TSA released a statement that said, "The child was screened along with all other passengers to ensure that he was not a threat to the aircraft."
A source close to the investigation told NBC News that the boy told a flight attendant that his parents were sitting in the back of the plane, but Hogan said the flight crew became suspicious at some point during the flight when they realized the boy "wasn't on the roster" of children travelling alone.
When the plane landed, Hogan said, "The Las Vegas Metropolitan Police and Child Protective Services there took the child into custody and were arranging his return to Minneapolis." As of Sunday, the boy remained in Las Vegas in Child Protective Services, according to the source.
The boy's mother said she thought he was at a friend's house and reported him missing, according to the source. Hogan said he was not listed as a runaway until after he had managed to travel to a different state.
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The boy has behavioral problems and was recently suspended from school, the source said. Police at the airport were familiar with the 9-year-old because he had caused problems there before, the source added.
In fact, Hogan said security footage and airport staff reports indicated the boy made an unaccompanied trip to the airport the day before his solo flight.
On both days, he arrived at the airport on light rail transit, said Hogan. On Wednesday, he visited baggage claim, took a bag that did not belong to him and had a bite to eat at a pre-security airport restaurant. He then told restaurant staff that he needed to use the bathroom and left the bag with them but did not return, Hogan said.
Hogan said, "Anytime there is a bag left unattended, that automatically raises a red flag," but said he was not sure whether or not restaurant staff communicated the incident or a description of the boy to the TSA.
"Obviously, the fact that the child's actions weren't detected until he was in flight is concerning," Hogan said, but added, "The airport itself isn't involved in any sort of passenger processing."
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Thirty-three million people travel through the Minneapolis-St. Paul airport each year, according to Hogan, who has worked there for 13 years. "I've never seen a case like this before," he said.
—By NBC News