Air France and Austrian Airlines have both had to cancel services after their flight plans were rejected by Russia.
EU leaders asked European carriers to avoid Belarusian airspace this week after a Ryanair plane was forced to divert and land in Minsk on Sunday.
Belarusian dissident journalist Roman Protasevich and his girlfriend were then arrested.
The UN’s civil aviation agency has said it will launch a “fact-finding” investigation into Belarus’s actions, and whether there had been any breach of international aviation law.
Russia is a strong ally of Belarus and President Vladimir Putin is set to discuss the unfolding crisis with Belarus’s leader of 26 years, Alexander Lukashenko, in the Russian resort of Sochi on Friday.
The decision to refuse entry to specific flights is the first move from the Kremlin over the diplomatic conflict. Other flights involving German carrier Lufthansa and Polish airline Lot have arrived as scheduled. Russia is yet to comment on the action it is taking.
The European Union and UK have banned Belarusian airlines from flying over their territories, and have said more sanctions are to come, including against Mr Lukashenko and other senior officials. EU foreign policy chief Josep Borrell says there are plans “on the table” to target key economic sectors.
The European airspace ban has forced Belarusian carrier Belavia to cancel 12 of its routes until 30 October, according to Reuters. The routes affected are Amsterdam, Barcelona, Berlin, Brussels, Frankfurt, Hanover, Kaliningrad, Milan, Munich, Rome, Vienna and Warsaw.
Belarus will lose out on millions of dollars a year in over-flight fees as a result of European airlines avoiding Belarusian airspace.
Russia’s move in support of Mr Lukashenko has led to the cancellation of at least four Air France flights between Paris and Moscow. Some passengers were rebooked on Russian carrier Aeroflot.
Two Austrian Airlines flights have been grounded – one passenger plane travelling from Vienna to Moscow, and a cargo plane travelling from Nanjing in China to Vienna.
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.