Russian state carrier Aeroflot and two other airlines cancelled several Russian flights to and from the Czech Republic on Tuesday after Prague withdrew permits for the flights.
An industry source told Reuters that the Czech Republic had taken the step after Moscow declined to approve a trans-Siberian flight route for Czech Airlines from Prague to Seoul.
Russia's Transport Ministry said talks were under way between Russian and Czech aviation authorities and it expected the issue to be resolved quickly.
Russia's budget airline Pobeda said it had cancelled two bi-weekly flights to the spa town of Karlovy Vary, while Ural Airlines suspended all flights between the Czech Republic and the city of Yekaterinburg and Moscow region's Zhukovsky.
Aeroflot said it had been forced to cancel flights SU2010/2011, SU2014/2015, SU2016/2017 and SU2018/2019 despite being ready to fly, but that two others would fly as normal.
The Czech Transport Ministry, which is in charge of licensing, did not immediately comment.
Later, Ural Airlines' general director said it had obtained permits for flights from Yekaterinburg and that those would fly as normal.