Thirty empty planes will be sent to Hurghada, and 14 will be sent to Sharm el-Sheikh, the Rosaviatsya agency said in a statement.
Moscow has said a total of 78,000 of its nationals are currently on holiday in Egypt.
"For security reasons, only hand baggage will be allowed on board," while cabin baggage will be transported by the Russian emergency situations ministry, it said.
"Two Ilyushin-76 planes should take off today for Egypt to transport the Russian tourists' bags," the ministry said today.
Irina Tyurina, a spokeswoman for the Russian Union of the Tourism Industry, had earlier told AFP earlier that Russian holidaymakers would not be required to return home if they did not want to.
The air transport agency said nine planes left Hurghada and four left Sharm el-Sheikh for Russia earlier today, adding that all were regular commercial or charter flights.
The number of Russian tourists travelling abroad has gone down significantly because of a plunge in the value of the ruble on the back of falling oil prices and Western sanctions over the Ukraine crisis.
Russia halted flights to Egypt after dismissing growing evidence that the plane might have been bombed by jihadists in an apparent act of revenge for Moscow's bombing campaign in Syria.
President Vladimir Putin's spokesman insisted the decision to suspend flights did not mean that Moscow believed the crash was caused by a deliberate attack.
Political analyst Stanislav Belkovsky said on Russian radio: "Putin understands that this is a terror attack, an attack which is a direct consequence of the military adventure in Syria which could not and cannot be justified from the point of view of Russia's national interests."
