Whitmarsh has admitted the team "lost its way" in development of the current car he has already conceded is flawed in many areas.
Small steps have been made since last weekend's horror performance in the season-opening grand prix in Australia in which Jenson Button and Sergio Perez finished ninth and 11th.
In qualifying for tomorrow's Malaysian Grand Prix, in tricky conditions as a heavy rain shower struck the Sepang International Circuit during the second session, Button and Perez fortuitously made it into the top 10.
However, the car's pace on a wet track was found wanting as the duo could only manage eighth and 10th respectively.
To aid their cause, Kimi Raikkonen was handed a three-place penalty for blocking Mercedes' Nico Rosberg, so both moved up a place and will start seventh and ninth.
It was a small crumb of comfort for Whitmarsh, who faced a grilling post-qualifying with regard to his position and the decision-making within the team.
"Clearly we've not done a good enough job, and there is a lot of analysis of that going on," said Whitmarsh.
"It's probably an excuse, but a decision was taken in August time last year to take some risk with this year's car.
"When you take those decisions you hope you develop a car that is going to be competitive at the start and have the ability to be developed over the course of the season.
"Clearly we lost our way in developing this car. Formula One is a relentless and unforgiving environment for mistakes, those you make at the track and those you make in coming to the track.
"The fact is we took too long to realise that."
Asked who made the final decision over this year's car, Whitmarsh refused to point any fingers, although took full responsibility.
"If people want me to lay blame at a particular door of someone in the team, or someone who may not be in the team now (referring to former technical director Paddy Lowe), that's never been my particular approach to management," added Whitmarsh.
"We as a team will work together, we as a team have to do a better job, and we as a team have to fix it.
"Am I responsible for what this team does? Yes. I don't make all the decisions, but you can't be in the position as team principal of McLaren and not accept responsibility.
"When the car is not successful, a lot of it inevitably gets focused on me. When the car is successful then there is credit elsewhere. That is the job and I'm relaxed about that.
"I've been around in the sport long enough, and personally involved in over 100 grands prix victories, so I know what it's like to win, and that's quite fun.
"I also know what it's like to not do a good enough job and I know if you are going to be team principal then you have to stand there and accept responsibility for it."
From Button's perspective, there was further frustration in the fact the car proved it also struggles in the wet, even though there were positive signs in such conditions last weekend in Australia.
"During Q1 and the first half of Q2 it appeared we're now a little more competitive in the dry than we were this time last weekend," said Button.
"We're still not quick, but the guys are doing a fantastic job to get everything they can out of our car.
"As for the race, when you've a quick car you never want it to rain.
"When you've got a less quick car, you do want it to rain.
"But today [Saturday] we didn't have great pace on the intermediates (wet tyres) in Q3 when it was raining, so all I'll say is as always we'll battle hard and see what the race brings."
On pole is Red Bull's reigning triple world champion Sebastian Vettel for the 38th time in his career, with Felipe Massa on the front row alongside him in his Ferrari for the first time in three years.
However, for the fourth successive race Massa lines up ahead of team-mate Fernando Alonso who starts third, with Mercedes' Lewis Hamilton fourth.
"I'm pretty happy with fourth place considering the conditions," said Hamilton.
"It's the second race on the second row for me and there are lots of positives to take out of the weekend so far."
Paul Di Resta starts 15th in his Force India after a mistake by the team with regard to strategy with the rain on its way, whilst Max Chilton starts 21st for Marussia.