Whitmarsh said the introduction of V6 turbo engines next year added even more costs to an already highly expensive sport, and more needs to be done to ensure the smaller independent teams can survive.
Along with the introduction of new engines and gearboxes, in-season testing will also be reintroduced next year, which alone is expected to cost teams $8-10 million. Some of the smaller teams may skip one or more of the tests for cost reasons.
"We have made some mistakes with introducing the new powertrains, we didn't control the costs enough, and the sport may well pay the price of that over the next 18 months," Whitmarsh said on Sky Sports late Friday from the Korean Grand Prix.
"We are not at crisis yet, but we have to be careful we don't wait for that crisis."
Previous efforts to reach a cost-control agreement through the Formula One Teams Association have failed because the bigger teams have been unwilling to handicap themselves for the good of the sport.
Red Bull was one of the teams that refused to make concessions, but principal Christian Horner still believed cost control was needed.
"It (FOTA) worked in the beginning, but it fell apart because self-interest was too strong amongst competitors," Horner said. "So you have to have strong leadership now in that respect.
"The cost of competing in Formula One at the moment is unimaginable and I can only imagine how it is at the other end of the pit lane."
One potential solution to reduce costs for smaller teams is the introduction of customer cars, in which they could buy chassis and aerodynamic parts from the big teams in the same way they now buy engines.
"Personally, if I was in charge I wouldn't propose customer cars as I don't think they are in the spirit of Formula One and they would be the death of many of the teams," Whitmarsh said. "But at the end of the day we are a business so if the regulations allow it then we would do it."