Whitmarsh believes that Grand Prix racing would benefit from having the kind of tripartite agreement that it has operated under for a number of decades now.
"You can have a purely commercial agreement [between the teams and Ecclestone], but if you are competing in the FIA championship then if you don't have a tripartite agreement it can be inherently confusing," Whitmarsh said.
"I think it would be good to have an agreement that involves all the teams, the commercial rights holder and the FIA. I hope we will work towards that."
Whitmarsh's comments come in the wake of suggestions from Ecclestone that the framework of a new Concorde Agreement could be different, with teams rather than the FIA laying down the regulations.
The way the current negotiations have unfolded - with Ecclestone trying to get all the teams signed up before pushing for agreement with the FIA - is also a departure from how things were done in the past.
Whitmarsh does not see any reason why Ecclestone will not involve the FIA in a final deal, however.
"In the past, the mechanism of negotiations was a simultaneous process that meant we all came together and signed. But that is not how some teams and the commercial rights holder have tackled this. It has been done in an incremental manner.
"Most of the teams are signed, those that have not signed are close to signing, and I think Bernie feels he is close to signing the remaining teams and signing a deal with the FIA – and we have to loop that together into a common agreement."