Egyptian officials did not publish a final report, which would have allowed BEA to better understand the differences in their conclusions, the French agency said.
It says the French report is "baseless", adding that "traces of explosives were found on the remains of passengers and parts of the plane".
"The BEA's proposals concerning further work on the debris and recorded data were not, as far as the BEA knows, followed up".
The French investigator said it stood ready to continue their collaboration with its Egyptian counterpart "should the latter restart the safety investigation into this accident".
On May 25, 2016, President Abdel Fatah al-Sisi received a delegation from the French National Assembly and offered his condolences to the French victims onboard the EgyptAir MS804.
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Because of this, it transferred the case to the Egyptian Prosecution Bureau for further investigation.
On Friday, the BEA said information gleaned from the flight recorders suggested "a fire broke out in the cockpit. causing the loss of control of the aircraft". No report has yet been released by the committee regarding the cause of the crash.
EgyptAir was not immediately available for comment.
In a press conference on the day of the crash, Egypt's civil aviation minister Sherif Fathy said a terrorist attack was most likely behind the crash. They spoke on condition of anonymity because they weren't authorized to brief journalists on the matter.
The BEA has also investigated the crash alongside Egyptian and American experts. After a bomb brought down a Metrojet plane carrying Russian holidaymakers home from the Red Sea resort of Sharm El Sheikh in October 2015, killing all 224 people on board, Egyptian officials initially denied widely held suspicions that a bomb caused the crash.