Stewart has been very critical of FIA President Max Mosley since the decision against McLaren in September, but has kept a low profile since Mosley stirred up considerable controversy by writing off the Scotsman as being "a certifiable half-wit".
Stewart was speaking in his role as the F1 ambassador for the Royal Bank of Scotland.
Sir Jackie was keen to point that he wished to avoid "unpleasantness between individuals" but said that he felt that there was a serious need for a rethink about the way F1 is governed and that there must be "the removal of any concern of genuine independence and impartiality in the governance of sport by the FIA".
Stewart again brought up the question of the $100m fine against McLaren and said that there was "an extraordinary imbalance between the magnitude of the penalty and the crime alleged to have been committed".
"What was the evidence?" he said. "There was no sensible answer that I have heard."
Stewart went on to say that power within the FIA is overly concentrated in the hands of the FIA President, that the World Council was never designed to be a judicial body and that the precedent that was set with the McLaren case has been worrying for the corporate world in F1.
"Corporate governance is an important business," he said, adding that he believes that the sport should be headed by a chief executive, "a captain of industry to be head-hunted. Someone who is not involved and not from within the FIA. It is not the job for a retired racing driver."
He argued that this was necessary "to ensure the very survival of the sport and the long-term future".
Stewart said that the FIA has done many good things in terms of safety but added that he was "concerned because my life has been F1 and I can see clouds of the horizon that could affect the future prosperity of the sport. The time has come to take stock."
The remarks will not go down well with the FIA. Grandprix.com