Several drivers on the 2013 grid owe their positions down to their financial backing, a situation that concerns Whitmarsh.
"I think, personally, it's sad to have so many pay drivers in Formula One," he told ESPN.
"The numbers have crept up, and while I'm sure it's good and exciting for those that can afford it, you would hope that in the premier form of motorsport worldwide that you wouldn't have to have pay drivers and that means there are some good young, professional drivers who can't get in and aren't getting in."
Whitmarsh believes that some teams are taking money for short-term gain, rather than the longer term benefit.
"If you look at the churn of drivers it's very low. One reason is because teams are conservative and don't take risks [in terms of drivers] and the risks that are taken materialise in instant revenue for the team but don't materialise in driver potential for the future. It's sad to say, but the reason that some of those guys are pay drivers, not all of them, but the reason that some are pay drivers is because they are actually and fundamentally not good enough to be in Formula One."
Whitmarsh's comments echo those of former Grand Prix racer Jarno Trulli, but McLaren's team principal is also concerned that the situation is not only prevalent in Formula One, but also in junior categories such as GP2, which hinders a driver's prospect of developing.
"One of the sad things is that in those junior categories, because those teams are making a business, the good teams get second- or third-year, well-budgeted drivers. I think if you said, in lower formulas, that a driver can only stay for two years in a junior category and each team has to have a rookie then I think you'd cleanse the system there."
Whitmarsh acknowledges the financial difficulties but adds that having a rookie in a junior category will prevent clogging the system.
"I think it's difficult in Formula One for us to say to some the teams that you can't have pay drivers because sadly they have become an important constituent of the budget. In the junior categories, having drivers that are around for four or five years because they can afford to be there just clogs up the system. If the top teams had to have a rookie then I think they'd be a fight over the good rookies at the bottom and they'd get sucked in because those competitive teams need them and they'd get accelerated through."