Although Stewart has long been critical of FIA president Max Mosley, in a lengthy interview with The Times on Monday he shifted his attention to Ecclestone – suggesting that big change was now vital at the top levels of F1 management.
"The era of big change is now essential because the sport has grown larger than either the governors or the commercial-rights holders. And that's just a fact," said Stewart.
"It has taken too long to achieve the things it should have achieved years ago and that other sports have long ago matured to, and other sports have prepared themselves more fully for the opportunities that have come their way."
He added: "I don't think Bernie can bring people in to help him in a transition phase. He has been so used to total control that if you look at his structure you have to ask yourself 'is there a successor?' and you would say 'no'.
"That is wrong. The commercial reality has to be recognised ... and there has (to) be continuity that the ageing process makes necessary."
Speaking about the way the sport's finances are shaped, Stewart also felt it wrong that 50 percent of the sport's revenues were pocketed by the commercial chiefs.
"Nothing is coming back into the sport," said Stewart. "The financial distribution of Formula One appears to have been sorted out by two people who have directed it in whichever way they have seen fit.
"Although this has been a significant benefit in some ways, it has also hurt the sport because the balance of contribution within Formula One is absolutely untenable.
"The teams have got all the capital investment, yet they get no more than 50 per cent of the revenues. The next largest capital investment is by the racetracks who currently receive little or nothing from the revenues apart from what they get for bums on seats.
"Hardly any of them receive anything from TV revenues or the circuit advertising or the title sponsorship or the commercial hospitality. How can they reinvest when they have little or no income outside of spectator attendance fees?"
And Stewart also maintained some criticism for Mosley, whom he has long called for to resign from his position as FIA president.
"I think Max should remove himself from the FIA completely and from motorsport and the motor industry," he says. "The FIA should replace him with somebody not from within its organisation or even within motorsport.
"They should go out and headhunt a CEO who is going to rebuild the structure in line with modern practice to satisfy the investors in the sport and to give the FIA total transparency."
