The unmanned machine appeared over Deschamps and his players as they went through drills at their team base in Ribeirao Preto prior to their departure for Porto Alegre.
Speaking ahead of France’s World Cup opener against Honduras on Sunday, Deschamps claimed the game’s governing body were looking into who was behind the stunt.
"Apparently drones are used more and more," said Deschamps.
"It’s not up to me, Fifa handles this and has been carrying out an inquiry; we don’t want any intrusion into our privacy. It’s very hard to fight this these days."
It is an unnecessary distraction for a France squad displaying the kind of unity which was sadly lacking on the ill-fated trip to South Africa four years ago which saw the squad go on strike.
Deschamps was asked about the events in Knysna but refused to make comparisons.
"You shouldn’t mention South Africa," he added.
"We’re now in another World Cup, we’re in Brazil, and were not going to be judged by what we did four years ago. It’s wonderful to have a good atmosphere here. We have the France supporters behind the team."