An alleged incident aboard a flight from France to Minnesota to Los Angeles prompted the FBI's involvement in the investigation, the source said.
The federal agency was notified Monday of the allegation, and agents were instructed to perform an assessment, the source said.
News of the investigation comes just days after Angelina Jolie Pitt filed for divorce from the actor, a decision her attorney said earlier this week was "made for the health of the family." Pitt, 52, and Jolie Pitt, 41, were married for two years before their split.
In the divorce document obtained by ABC News, the estranged couple's date of separation was listed as Sept.
Jolie Pitt has asked for physical custody of the couple's six children, Maddox, 15, Pax, 12, Zahara, 11, Shiloh, 10, and twins Knox and Vivienne, 8.