The allegation involved unruly behavior by Pitt while airborne with his child present, according to the source, who would not elaborate.
The Los Angeles County Department of Children & Family Services is now conducting an investigation into Pitt's conduct while the family was flying on a private jet from France to the United States, the source said Thursday.
TMZ first reported allegations that the
The website reported that an anonymous report was sent to the family services department.
On Thursday, the LAPD denied claims that its detectives were investigating child-abuse allegations involving Pitt.
"LAPD is not handling any reports or allegations into child abuse for Mr. Pitt," spokeswoman Officer Jenny Houser said Thursday.
The department's Juvenile Division, which would handle high-profile child-abuse cases, has no open investigation into Pitt, Det. Meghan Aguilar said.
Aguilar said LAPD officials called TMZ to inform them they were not investigating Pitt.
"I don't know if they just don't believe us," she said.
DCFS spokesman Armand Montiel said he could not comment on whether the department was investigating.
"The law does not allow us to confirm or deny the subjects of our investigations," he said.
Jolie's attorney, Laura Wasser, declined to comment.
Late Thursday, FBI spokeswoman Laura Eimiller issued a statement, saying, "The FBI is continuing to gather facts and will evaluate whether an investigation at the federal level will be pursued."
Jolie filed for divorce from Pitt on Monday, citing irreconcilable differences, but didn't elaborate on what those differences are.
She is seeking sole physical custody and joint legal custody of their six children: Maddox, Pax, Zahara, Shiloh and twins Knox and Vivienne. In the Los Angeles County Superior Court filing, Jolie said she was willing to give her husband visitation rights.
The separation date is listed as Sept. 15. Jolie and Pitt were legally married Aug. 14, 2014, after a two-year engagement.
The couple met while working on the movie "Mr. & Mrs. Smith" and got together in August 2005.
Jolie is seeking property in the divorce, including miscellaneous jewelry and other personal effects, her earnings and accumulations from and after the date of separation and "additional separate property assets and obligations of the parties, the exact nature of and extent of which are not presently known."
In a 2015 interview with the Telegraph, Pitt gushed about parenthood.
"Everyone talks about the joy of having kids — blah, blah, blah. But I never knew how much I could love something until I looked in the faces of my children," the actor said, describing his family unit as sharing "a lot of love, a lot of fighting, a lot of refereeing; a lot of teeth-brushing and spilling … Chaos, total chaos. But so much fun."
It's unclear what effect, if any, reports of the incident would have on the couple's pending divorce.
"I would think that a single incident of someone misbehaving or screaming or pushing, where there was no injury and no suggestion of this being habitual, is very unlikely to have a big effect on who gets custody and who gets visitation," said Scott Altman, a USC law professor and family law expert.
When there are reports of habitual abuse, those could lead to monitored visitations, but the behavior being alleged in this instance doesn't appear to fall under that category, Altman said.
"On the other hand, nobody likes to have their dirty laundry aired publicly," he said.
Divorces can lead people to "behave badly" and threaten to release embarrassing personal details of their spouse as leverage to gain a fast or rich settlement, he said. Other times it's simply venting without a goal in mind.
"I don't think there's any way to presume based on rumors getting started that facts were leaked by one of the parties. It could be a witness or a third party. I wouldn't assume quickly that it's a rumor started for strategic purposes," Altman said.
"I think judges have to ask, 'What evidence do we have? Is anything being alleged even relevant?' If nobody got hurt, a judge might say this is not even by itself going to be relevant to this decision."
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8 p.m.: This article was updated with a brief statement from the FBI.
1 p.m.: This article was updated with details from a law enforcement source.