This may clear the 52-year-old actor on abuse allegations made when his wife Angelina Jolie filed a divorce on the grounds of 'irreconcilable differences'.
Sources say the incident was anonymously reported to child protection authorities by either someone on board the plane or a member of the tarmac ground crew.
The A-listers Wednesday in France in August two years ago, but have been a couple since 2004.
Brad Pitt is at the centre of an FBI investigation into child abuse after an alleged incident took place on a flight with his eldest son Maddox.
The L.A. County Department of Children and Family Services told ET, "We have very strict confidentiality laws and the laws do not allow us to confirm or deny the subjects of our investigations".
Several media outlets reported that on September 14, an intoxicated Pitt became violent with his children while flying on a private jet from France to Los Angeles.
The couple separated September 15, just one day after the incident, and Angelina filed for divorce this week.
The actor and his 15-year-old son were at odds for unknown reasons, but Pitt did not touch the teenager at any time claims the source.
A source close to Pitt told USA Today that the Fight Club star meant to cooperate fully with any investigation and that he believed the child abuse allegations were baseless.
County social workers are the primary investigators and have talked to the family, the source said.
In a statement, the Federal Bureau of Investigation confirmed it was aware of allegations involving an "aircraft carrying Mr Brad Pitt and his children".
It said it was evaluating whether to launch an investigation.
Meanwhile, the Los Angeles Police Department has forcefully denied claims that it was investigating any complaint against Pitt: "LAPD is not handling any reports or allegations into child abuse for Mr. Pitt", spokeswoman Jenny Houser told the Los Angeles Times.
While Pitt will be represented by attorney Lance Speigel, whose clients include Michael Jackson, Charlie Sheen and Eva Longeria; Jolie's legal team consists of well-known divorce lawyers Laura Wasser and Robert Offer.