The actor, 52, was one of a string of celebrities in LA who were forced to flee the wildfires which have devastated homes and killed at least 24 victims.
It has emerged authorities were photographed outside his $US20 million ($A32 million) home in Brentwood, California, after he briefly returned to the property, which survived the LA infernos.
A representative for the FBI press office told Page Six about the visit: "Members of the FBI's Ground Intercept task force are conducting activity in the area of the Palisades Fire relative to unauthorised drone activity.
"Agents and our local partners may be visible throughout the area, including at various residences, for this reason."
A source added to the outlet: "FBI agents were at Affleck's home to see if he had CCTV footage of a private drone which damaged a super scooper, one of the firefighting aircrafts."
Affleck has been forced to evacuate his Brentwood property after going back to check on his bachelor pad.
An insider told Page Six earlier this week about his quick return to the house: "Ben's home is still under evacuation order but he feels so grateful his property is safe for the time being.
"Ben knows many people who unfortunately lost their homes. He has seen a lot of devastation and it's beyond tragic.
"This situation is devastating to so many and Ben is reaching out to anybody he can to help."
When the actor initially left the home earlier this week it emerged he went to seek shelter at his ex-wife Jennifer Garner's home.
He was photographed driving to the 52-year-old actress' home with his arm hanging out of the window of his black SUV on Tuesday night.
Jennifer and her and Ben's children – Violet, 19, Seraphina, 16, and 12-year-old Samuel – were reported to not have been ordered to evacuate the area yet, but they were said to be on standby.
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