The Brazil-to-France flight plunged into the Atlantic Ocean on June 1, 2009, killing all 228 people on board.
It makes new recommendations for the training of pilots and certification of planes, on top of 25 safety recommendations made in an initial report last year.
Some safety recommendations have already been implemented but it could take years for others fully to come into effect, chief investigator Alain Bouillard told reporters.
The international aeronautic community will likely focus on the crew's loss of awareness of what was going on, he said.
The use of automatic systems on planes has improved safety overall, Bouillard explained, but "when it comes down to it, safety will always be based on the capacity of the pilots and the signals which they are given, which they have to understand and react to."
It was an "exceptional" inquiry because of the scale of the disaster, the number of countries involved and the difficulty of locating the plane's data recorders, he said. The intense media coverage of the crash added to the pressure, said Bouillard.
It's a crash that never should have happened, said CNN's aviation specialist Richard Quest. The industry will be studying the human factors of the crew on the plane for many years to come.
The agency said its report does not examine the issue of responsibility for the crash, which is the subject of a separate judicial inquiry.
It took four searches over the course of nearly two years to locate the bulk of the wreckage and the majority of the bodies in a mountain range deep under the ocean.
The aircraft's voice recorder and flight data recorder were recovered from the ocean floor in May 2011 after an extensive search using miniature submersible vehicles.
The Bureau of Investigation and Analysis said the data indicated that Flight 447 crashed because the aircraft's speed sensors gave invalid readings.
Last year's report from the bureau said the airplane climbed to 38,000 feet when "the stall warning was triggered and the airplane stalled." It then descended, crashing into the Atlantic. The descent lasted three minutes and 30 seconds, and the engines remained operational, the report said.
Studies of the debris and bodies found soon after the crash led the French agency to conclude the plane hit the water belly first, essentially intact. Oxygen masks were not deployed, indicating that the cabin did not depressurize, the bureau said in a 2009 report.
Flight 447 was passing through an area prone to volatile and dangerous weather known as the Inter-tropical Convergence Zone when it went down. The zone is a belt of low pressure that wraps around the planet. Clouds and storms form along it because it is literally where the winds of the world's hemispheres meet.
The Bureau of Investigation and Analysis' previous report also raised questions about the training of the pilots on that flight.
The recorders revealed the pilots had failed to discuss repeated stall warnings and "had received no high altitude training" to deal with the situation, the bureau said.
The pilots got conflicting air speed readings in the minutes leading up to the crash and, after the stall, responded by pointing the nose upward, rather than downward, to recover.
They failed to regain control of the aircraft, and no announcement was made to the passengers before it plummeted from the sky.