Russia denied entry to two European airlines because they decided to avoid flying over Belarus to get to Moscow.
Air France and Austrian Airlines have both had to cancel services after their flight plans were rejected by Russia.
Some airlines are avoiding Belarusian airspace in protest after the government there forced a Ryanair plane to divert and land in Minsk on Sunday.
A Belarusian dissident journalist and his girlfriend were then arrested.
Russia is a strong ally of Belarus, and has remained steadfast in its support of the former soviet nation and its government.
It is the first move from the Kremlin over the diplomatic conflict between Belarus and Western countries. Russia is yet to comment on whether all flights will be denied entry if they avoid the airspace.
The European Union and UK banned Belarusian airlines from flying over their territories, and have said more sanctions are to come, including against Belarus’s president of 27 years, Alexander Lukashenko, and other senior officials.
The European airspace ban has forced Belarusian carrier Belavia to cancel 12 of its routes until 30 October. The routes affected are Amsterdam, Barcelona, Berlin, Brussels, Frankfurt, Hanover, Kaliningrad, Milan, Munich, Rome, Vienna and Warsaw.
A number of European airlines have stopped flying to or over Belarus, a move which directly affects the country’s revenue, because airlines pay to use a country’s airspace, amounting to millions of dollars per year.
In response, Russia rejected the flight plans of the Air France and Austrian Airlines planes, which showed them circumnavigating Belarus.
Austria’s foreign ministry said Russia’s actions were “absolutely incomprehensible”.
The French ministry of transport told AFP news agency that “the principle of reciprocity… must be respected”.
Tracking website Flightradar24 showed little activity in the skies over Belarus on Thursday, except for Belarusian and Russian airlines.