Primary physical custody of the children means that Sean Preston, 22 months, and Jayden James, 10 months, would reside with their father and that their mother would have visitation rights.
The source said that the 25-year-old singer must respond to the order at a closed court hearing.
"When they are with him, he is going to shield his children from unwanted media attention," Kaplan told the AP. "You will not find a picture of Kevin parading with the children out in a public place."
Spears has made headlines recently for bizarre behavior, including a magazine interview in which her dog defecated on a designer dress.
Federline and Spears' divorce was finalized July 30.
By Amy Bonawitz