F1 supremo Ecclestone warned again in Bahrain that Mateschitz - the billionaire owner of reigning world champions Red Bull - is so unhappy with the new face of the sport that he could quit.
"If he wanted to stop, he'd stop," the 83-year-old told the British broadcaster Sky.
"He is not happy with the way the sport is being run at the moment, and this is the sort of thing that could tip him over," Ecclestone added.
Together with Red Bull but also Ferrari and the other top teams in the decision-making 'strategy group', Ecclestone has already killed FIA president Jean Todt's plans for mandatory budget caps in 2015.
As Ecclestone has six votes, the top teams have another six and Todt has only six, "It's mathematics," the disappointed Frenchman admitted. "No more cost cap."
He said he will now push cost reductions through for 2015 via the sporting regulations, but the struggling smaller teams are unhappy to have been left out of the voting process altogether.
"You can't enrich and empower certain very strong teams, disenfranchise the rest and expect us to be happy," Force India's deputy boss Bob Fernley is quoted by the Guardian.
Fernley said Ecclestone and the top teams wanted to kill the budget cap because the smaller teams could now fold, paving the way for "customer cars".
"Yeah, I'd like to see that," Ecclestone admitted when asked about the idea of the top six teams selling chassis to the bottom half of the grid.
"Whether it would work or not (I don't know)," he added.
In the end, it probably all comes down to the old 'Ecclestone versus the FIA' battle for control of formula one.
Ecclestone insists the rumours he wants full control of F1 in his own hands are "nonsense". Perhaps the real plan is 'GP1'.
Told that support series GP2 is not only a vastly cheaper category, but also now with cars almost as fast as the 'green' F1, and certainly louder, Ecclestone fully agreed.
"Maybe we should turn GP2 into formula one," said Ecclestone, who already controls the GP1 trademarks. "It would certainly cost a lot less. We'd certainly have a lot more teams.
"So maybe what we're talking about is a 'super GP2'," he added.