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Jean Todt has confirmed that the FIA have brought in independent auditors in response to complaints by Force India and Sauber.
The two teams brought a case to the European Union in September regarding Formula 1's rules and the division of revenues, alleging that the sport currently breaches European competition laws.
FIA president Todt says he believes the organisation fulfils European corporate governance laws, but wants the FIA's internal practices to be fully transparent and above board, in the wake of the Force India and Sauber action and the corruption claims made against football's world governing body Fifa and athletics' governing body the IAAF.
"Unfortunately, some global sporting organisations have been facing some problems, and I can only be sorry for them," Todt told the Autosport International Show.
"Am I comfortable about the way our organisation is structured and run? Yes, I am, and I am very proud of all the people involved with it.
"Saying that, I feel if you are aiming for excellence then you can always try to do better.
"I have asked a specific audit company to have a look at our organisation, and if they feel they can advise on some improvements, then I’m very happy to take them on board."
Todt says F1 is also considering bringing back mid-race refuelling to the sport, with the rule change to be discussed during a meeting of the sport's Strategy Group in Geneva on Monday.
Mid-race refuelling was dropped in 2010, and proposals to bring it back for the 2017 season were dropped because of negative feedback from a previous meeting of Formula 1's Strategy Group.
"We [will] re-address - is it right not to have refuelling?" Todt told Reuters.
"We are talking about 50,000 euros a year for refuelling costs. If it is good for the show, I'm in favour of reducing the cost, but that is not a key point in the global costs of Formula 1.
"At least we should discuss it."