They said onboard recorders suggested that the blaze had spread rapidly through the plane.
The findings contradict Egypt’s earlier statements that explosives had been found on victims’ remains, suggesting the aircraft had been bombed.
Sixty-six passengers and crew died when the flight from Paris to Cairo came down over the eastern Mediterranean.
France’s civil aviation accident bureau, known as BEA, said in a press release on Friday that “the most likely hypothesis is that a fire broke out in the cockpit while the aeroplane was flying at its cruise altitude and that the fire spread rapidly resulting in the loss of control of the aeroplane”.
The agency said that the crew could be heard discussing a fire on the cockpit voice recorder and that systems on board had detected smoke inside the aircraft.
Egyptian officials previously said that the crash – which came seven months after a Russian plane was brought down by a bomb over the Sinai peninsula – was likely to have been a terrorist incident.
The BEA has said it is awaiting Egypt’s final report into the crash to understand the differences in their conclusions.
Thirty Egyptians, 15 French nationals and one Briton were among the dead.