An investigation into whether or not Brad Pitt was abusive toward his son on a private flight in September has been closed, a representative for Angelina Jolie told FOX411.

"The job of the [Los Angeles County Department of Children and Family Services] is to make sure the children are in a safe and secure situation. As we said earlier this week, childcare professionals encouraged a legal agreement accepted and signed by both sides that was in the best interest of the children," Jolie's rep told us. "Angelina said from the beginning that she felt she had to take action for the health of the family and is relieved that after their 8-week involvement, the DCFS is now satisfied the safeguards are put in place that will allow the children to heal."

A source with knowledge of the situation told us that Pitt and Jolie agreed to a custody agreement "encouraged by childcare professionals." The agreement gives Jolie full custody of the pair's six children with "therapeutic visits" allowed for Pitt. However, reports earlier this week indicated the arrangement is being contested as Pitt filed for joint custody in court Friday.

California law favors joint custody, although details about custody arrangements are rarely made public in celebrity divorce cases.

The source insisted that Jolie never accused Pitt of child abuse nor did she call the DFCS on her estranged husband.

A department spokesman said the agency could not confirm or deny it investigated Pitt.

A representative for Pitt declined comment. During a Q&A for his new movie "Allied," Pitt said, "It's really sweet, everyone has been really kind out here. It's really nice to have all the support."

Pitt and Jolie were married for two years and together for 12 years after becoming close while filming 2005's "Mr. & Mrs. Smith."

The Associated Press contributed to this report.