The Islamic State group (IS) claimed responsibility for bombing the plane carrying Russian holidaymakers in October 2015, killing all 224 people on board.
The wreckage has been transported to Cairo airport and will be pieced together "to determine the starting point for the (plane's) disintegration", an aviation ministry statement said.
IS has claimed it smuggled a bomb inside a soda can onto the plane in a Sinai resort airport, in response to Russian air strikes in Syria.
French and Irish experts were also expected in Cairo for the investigation, the ministry said, adding that the aircraft had been designed in France and registered in Ireland.
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The bombing prompted Russia to suspend flights to Egypt, in a blow to the country's tourism industry.
Egypt was hit by another aviation disaster in May this year when an Airbus A320 flying from Paris to Cairo went down in the Mediterranean.
All 66 people on board were killed.
Investigators said the black boxes and the wreckage pointed to a fire on board, but they have not yet announced the cause of the crash.