Terms were agreed over the weekend between Newcastle and Lyon, but as yet the deal has not been finalised.
Now Aulas has told L'Equipe that the deal is in some doubt, and is quoted as saying: "Gomis? I am very disappointed the operation could not be sorted out with Newcastle.
"I have filed a complaint for 'destabilisation'. Things will be settled in front of the appropriate committee (of the French Professional Football League).
"It is a complete disservice to Bafe. He is a player that we respect. It completely flipped over with Newcastle.
"Personally, I am very pessimistic (about Gomis). If we won't find any solution by August 30th, Bafe will join back with the group as it is us who pay him and prepare him physically.
"It is in everyone's interest for all of us to find a positive outcome."
Having already concluded a deal for Loic Remy on loan, Newcastle were looking at bringing in another striker, with bids in for Gomis as well as Aston Villa's Darren Bent.