The F1 chief executive is worried the sport will lose some of its appeal to fans when next year's engines fail to live up to the dramatic noise of the current V8s.
The grand prix circuit promoters, led by Australia's Ron Walker, are also worried.
"As Bernie will attest," Walker told F1 business journalist Christian Sylt, "it (the V6) sounds like a lawnmower engine, and we will be fighting this tooth and nail."
Less publicly worried are the engine makers themselves, who see the new regulations as a welcome step into the automobile's modern era.
It is also expected that Honda could now return to F1, amid rumours Volkswagen and Toyota are also interested in the V6 rules.
But Ecclestone thinks the radical change of regulations is actually a risk for the suppliers.
"The danger is that what will happen is what always happens with the manufacturers, which is that if it doesn't work they will stop," he told Autoweek.
And another risk is that the 'lawnmower' tones of the V6s will also drive the spectators away.
"What Ron (Walker) is saying is that you have to make sure that the engines will make it to 16,000 revs," said Ecclestone.
"That was agreed and now we know they won't rev to anything like that. The fuel flow has been agreed so even if you have big tanks it still can't rev (to 16,000)."
Admitting it is not his preferred option, Ecclestone nonetheless revealed that artificially enhancing the V6 engine sound is a possibility.
"Maybe we can make them sound like the current engines," he said.
Walker added that in 2011, "(FIA president Jean) Todt told me in Australia that the next thing is they are going to have a hybrid.
"I said 'what about the noise' and he said they will put a squeak box on the back of the car. God almighty!"