The origin of these traces remains unclear and Egyptian judicial authorities did not allow French investigators to examine the debris in detail, Le Figaro said, citing a source close to the investigation.
Egypt wishes to write a joint report with France to validate the presence of TNT on the debris. France has refused to do this because the investigators were not able to carry out an adequate inspection to determine how the traces could have got there, Le Figaro said.
A spokesman for the French national police declined to comment.
EgyptAir flight MS804, an Airbus A320, plunged into the eastern Mediterranean en route from Paris to Cairo on May 19.
All 66 people on board were killed, including 15 French passengers. The cause of the crash remains unknown.
Audio from the flight recorder of the crashed aircraft mentions a fire on board the plane in its final moments, the investigation committee said in July.
Earlier analysis of the plane's flight data recorder showed there had been smoke in the lavatory and avionics bay, while recovered wreckage from the jet's front section showed signs of high-temperature damage and soot.
