Canada’s football association was “responsible for failing to respect the applicable FIFA regulations in connection with… the prohibition on flying drones over any training sites”, FIFA said.
It also handed down a fine of 200,000 Swiss francs ($226,000).
The ruling is a hammer blow to Canada’s hopes of defending the Olympic title they won at the Tokyo Games three years ago.
It leaves them on minus three points in Group A before they play hosts France on Sunday in Saint-Etienne.
They beat New Zealand 2-1 in their opening game on Thursday but the deduction means they now face having to win their next two matches to stand any chance of reaching the quarter-finals.