Chad Cameron Camp, 26, was sitting next to an unaccompanied minor on a half-empty American Airlines flight from Dallas to Portland, Ore.
An attendant had asked if he wanted to sit somewhere with more room but he declined.
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But about 30 minutes into the flight an attendant serving drinks noticed Camp's hand on the girl's crotch and a tear falling down her cheek, according to the complaint.
Flight attendants then separated Camp from the girl and when the plane landed Camp was arrested and charged with abusive sexual contact, according to the FBI.
The girl's attorney says the airline failed to protect her.
The victim's family had paid an extra $300 so that the girl would be allowed to travel by herself.
The lawyer argued that Camp should not have been allowed to sit next to the unaccompanied minor, citing airlines with policies that bar men from sitting next to children travelling alone. Camp's attorney entered a 'not guilty' plea on his behalf.
He also disputed those who are saying the flight attendant saved the young girl, saying: "If I have my tray table down or my seat back two inches during the improper time, those guys are going to be on me immediately."
"This girl got abused for 30 minutes and no one was to be found."
In a statement to CNN, American Airlines said: "American cares deeply about our young passengers and is committed to providing a safe and pleasant travel experience for them."