All 224 people on the Airbus 321 - most of them Russians - died when it came down over the northern Sinai peninsula.
The country observed a day of mourning on Sunday after its worst air disaster.
Russian Air Transport Agency head Aleksandr Neradko has said the airliner disintegrated at high altitude.
The Kogalymavia plane was carrying 217 passengers, including 25 children, Russian transport authorities said. There were seven crew members on board.
Four of the passengers were Ukrainian nationals and one was from Belarus.
A Russian government transport plane carrying the remains of the victims landed at St Petersburg's Pulkovo airport on Monday morning.
Vehicles later began transporting the bodies to the city's crematorium for the identification by the relatives.
A second flight with more bodies is expected to arrive in St Petersburg in the evening.
Russia says it will pay compensation to the victims' families and help organise funeral procedures.