The agency's statement said the companies have ignored repeated demands that they repay their debts, and that this is damaging plans for the modernization and improvement of air traffic control.
It said Krasnoyarsk Airlines has outstanding debt of 7.43 million rubles ($280,000) Dalavia 4.7 million rubles ($180,000), and Interavia 1.8 million rubles ($69,000).
Siberia-based Krasnoyarsk Airlines said it will repay its debt to the air navigation service on Wednesday.
"We acknowledge the debt. It will be fully repaid today. All obligations to passengers will be fulfilled, and there will be no cancellation of flights," a spokesman for the airline said.
The other two airlines were unavailable for comment.
The move could have a crucial impact on Russia's air transportation, as the three airlines are major regional air carriers, particularly in Siberia and the country's Far East.
Alexander Neradko, head of the Federal Air Transportation Agency, said earlier that Russia currently has one of the lowest air transport tariffs in the world, and that the civil aviation authority plans to increase tariffs for air navigation services provided to domestic and foreign airlines.
