Ecclestone, the sport's commercial supremo and shareholder, told Britain's Daily Mail newspaper last month that Formula One was the worst it had ever been and he would not pay to take his family to watch it.
The 85-year-old British billionaire subsequently told Reuters that his comments were meant as a wake-up call to teams ahead of a key meeting of the core Strategy Group to discuss 2017 rule changes.
"I wasn’t talking down the sport at all, quite the opposite. I was trying to sort of explain that unless we did something that’s the way we’d be going," he said.
Zetsche told reporters at a Mercedes E-class presentation at the former Portuguese Grand Prix circuit that he could not comprehend why Ecclestone would make such comments.
"At the Geneva Motor Show I was not going on the stage to say I would never drive a Mercedes and customers should better not do it," he said.
"I don't understand how someone who is not only the CEO but partial owner of that product talks that way about this product," added the German.
"If he feels about that, it should be discussed internally how to change it, but not as a sales pitch."
Ecclestone has been at loggerheads with Mercedes, whose British driver Lewis Hamilton is chasing a fourth title this season, and their closest rivals Ferrari, accusing the manufacturers of wanting to control the sport.
The two carmakers provide power units to eight of the 11 teams, meaning that their customers generally vote in line with them in key meetings.
In the same Daily Mail interview, Ecclestone had accused Mercedes and Ferrari of running an illegal "cartel".
The season starts in Australia on March 20.
(Writing by Alan Baldwin in London; editing by Toby Davis)
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