The Woking squad has made it clear that its new MP4-28 is a major departure from the 2012 car, saying that the focus was on long-term development potential even if it came at the expense of early-season pace.
Reliability was an issue for McLaren last season, notably when Lewis Hamilton retired from the lead in both Singapore and Abu Dhabi.
But Whitmarsh said the level of change McLaren had opted for this winter inevitably raised reliability questions.
"With a new racing car you can never be as confident as you would like to be, because if it's stable and reliable, typically you want to change it to make it quicker, lighter, more aerodynamic or something," he said.
"We have given ourselves a platform which is new to ensure that we have got development opportunity over the course of the season.
"In so doing, it makes it more challenging after 5000kms of running to go into the first race as comfortable about reliability as you want to be."
He added that McLaren had tried to address 2012's specific technical problems, but did want to get fixated on reliability.
"We have been working hard with Mercedes-Benz on some of the issues that we saw last year and internally as well," Whitmarsh said.
"So I think we are constantly vigilant but we mustn't become so obsessed by the pursuit of reliability that we don't change the car.
"Clearly, we have taken some risks in changing the car from last year. We finished the last few races with the quickest car.
"It would have been very easy to have continued to develop that car.
"We'd have made it quicker still for the start of this year, yet we have made a lot of changes to the overall package and we have done so in the belief that you have to be competitive over 19 races, to be able to develop it."