EgyptAir received a notification from Moscow's Domodedovo International Airport that the flight on early Saturday was cancelled through a company manager at the airport, Civil Aviation minister Hossam Kamal said in a Friday ministry statement.
Russian authorities have still not officially informed Egypt of their reasons to cancel EgyptAir flights to Moscow starting on Saturday, according to Kamal.
As per the airport's notification, EgyptAir decided to halt the Saturday flight and re-book other flights from Cairo for the passengers. The passengers on the arriving flight to Cairo from Moscow will also have their flights re-booked.
The Russian Aviation agency Rosaviatsiya formally notified Domodedovo airport, where EgyptAir flights arrive, that the ban is effective starting Saturday, said the airport spokesman Alexander Vlasov.
Egypt operates three weekly flights from Cairo to Moscow on Saturdays, Tuesdays and Thursdays.
Official phone calls are being conducted on a high-level between officials from both countries in order to clarify the matter and to understand why the flights were halted as was reported by news agencies, Kamal said.
The Egyptian aviation authority is also conducting calls with the Russian side to understand the reasons behind the decision of which it was not officially notified of.
The reasons for Russia's cancellation of EgyptAir flights to Moscow are still unknown.
A source told Russian news agency Interfax that the absence of an aviation safety programme is the reason why the Russian aviation agency Rosaviatsia banned EgyptAir flights to Russia.
Russian ambassador to Egypt Sergei Kerbachenko told Al-Hayat channel on Friday that the halt was a temporary security procedure.
Kamal said the Russian authorities asked their Egyptian counterparts for a Russian translation of the operations manual for flights between Egypt and Russia. A translated manual was submitted on Thursday in coordination with the Egyptian embassy in Moscow.
On Friday Russia's state aviation agency banned Egypt's national carrier from flying to Russia, a move that follows the suspension of all Russian flights to Egypt after a deadly crash on 31 October that killed 224 people on board.
The largest Russian airline Aeroflot will stop flights from Moscow to Egypt starting November 18, Russian news agency Interfax reported.
Another airline from Aeroflot group, Orenburg, will stop flights from Russia to Egypt on December 1.