Led by car-makers Renault, BMW, Honda, Daimler-Chrysler and Toyota, the Grand Prix Manufacturers' Association (GPMA) is demanding a greater share of F1 income.
And although relations between the GPMA and FIA president Max Mosley have warmed, Stoddart fears the worst.
"It is looking increasingly more obvious, the manufacturers have made a very clear statement that they want a fair and equitable Formula One,” said Stoddart.
"We agree with that statement and it is going to give rise to the two championships which everybody fears.”
Stoddart, who is selling his Minardi team to Red Bull at the end of the season, is considering returning to team ownership once the dust has settled on any split.
Red Bull and Ferrari are the only parties that have already agreed to an extension to the Concorde Agreement, due to run out at the end of 2007.
