"We'd have to run as it is. You can't suddenly make people run more cars," he told reporters at a lunch to promote this year's French Grand Prix. "If they didn't enter the Championship it would be a different story."
The Honda-powered team are waiting to hear their fate after the governing FIA, asked an appeal hearing in Paris to exclude them from the Championship.
The FIA said BAR had set out "deliberately to gain an illegitimate and unfair advantage over other teams, an act prejudicial to the interests of the competition and to the interests of motor sports generally".
BAR have denied accusations that Briton Jenson Button drove an underweight car equipped with a hidden, secondary fuel tank to a third-place finish at the San Marino Grand Prix.
The verdict is due on Thursday.
Under the confidential commercial agreement that governs Formula One, teams must make up the shortfall if there are fewer than 20 cars entered at the start of a season. There are currently 20, including BAR.
However McLaren, Red Bull and Jordan already run three cars in Friday practice as part of regulations aimed at helping teams that finish the Championship outside the top four.
Ecclestone, who fell foul of the technical regulations himself while owner of the Brabham team in the 1980s, hoped BAR would be cleared but questioned their position.
"I'd rather see them found not guilty," he said. "But with the information that's available to almost everybody, you would have to assume that what they did was an infringement of the regulation."
The FIA are also seeking a one million euro fine ($1.29 million) for BAR. Ecclestone said such a financial sanction could not stand on its own.
"If you can do that, why doesn't the team at the beginning of the year give over a cheque and say 'If I'm caught, cash the cheque," said Ecclestone.
He suggested one alternative might be to prevent the team from scoring constructors' points while allowing the driver to continue scoring in the Championship.
"You'd have to exclude the points the driver has made (until the sanction) and all the points for the team for the whole year. There's a million things you can do," he said.
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