France is sent before European Court of Justice over 10M-euros given to low-cost airlines Ryannair and Transavia to use regional airports.
After a lengthy strike earlier this year, pilots narrowly voted in favour of plans to develop the airline's low-cost operator Transavia.
After a costly pilots' strike last month, initial agreement has been reached for crews flying Transavia planes to retain Air France benefits.
Dispute could wipe out second quarter profits but some say that failure of striking pilots to win clear victory is good news for airline's future.
The airline denied transport secretary's comments that it had dropped its plan to delocalise low-cost arm and which sparked pilots' strike.