The 41-year-old actress is believed to have "fully cooperated" with the investigation department, who also spoke to "some of her kids", reported Us Weekly.
"The agents wanted a breakdown of everything that happened from when the plane took off to when it landed. They're looking into charges of assault," a source said.
The source added that the FBI "will likely investigate for another few weeks" and will subsequently present the case to the prosecutor, who will further evaluate the matter.
According to another source, both stars do not want get involve in any kind of court case as "everything the FBI and DCFS investigate, will potentially be made available to the public".
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It was earlier reported that the "Fight Club" star got "verbally abusive and physical" with the his kids.
Jolie also filed for divorce from him on September 19, citing irreconcilable differences, and requested sole custody of the kids under the influence of alcohol during a flight from France to California on September 14.