It came after a former acquaintance of John Mark Karr in California told authorities that he threatened to kill her if she revealed his attempts to form a cult of little girls to have sex with him.
Sandy Springs, Ga., Police Lt. Steve Rose said Tuesday that officers issued a restraining order last week at the request of San Francisco authorities.
The order was taken out by 19-year-old Samantha Spiegel, who claimed that he made "ongoing death threats" and "threats of sexual exploitation to children."
Rose said the order was served June 3.
Karr's 89-year-old father, Wexford Karr, told The Associated Press on Monday that his son stayed at his home in northern Atlanta last week but left "in the middle of the night" a couple of days ago. Wexford Karr said he was not aware of the restraining order or the allegations against his son.
JonBenet, a 6-year-old child beauty queen, was slain in 1996 in her parents' home in Boulder, Colo.