All the 228 people on board were killed when the airline’s Flight 447 from Rio de Janeiro to Paris came down in the Atlantic Ocean on 1 June that year.
The preliminary charges pave the way for further investigation.
The move comes a day after the judge filed similar charges against Airbus, which manufactured the plane. The cause of the accident is still unknown.
Sensors on the aircraft sent faulty speed readings to pilots, but Airbus says no one can know for sure what happened as the so-called “black boxes”, which monitored events during the flight, have not been recovered.
Next week, a fourth attempt to find the voice and data recorders will get under way.
The search, financed jointly by Air France and Airbus, will involve dives to depths of up to 4,000m (13,120ft) and use special robots to examine the ocean floor between Brazil and West Africa.