The Japanese manufacturer announced last week that it would return to the sport in a "joint project" with McLaren.
Whitmarsh believes the deal will guarantee McLaren has the resources and structure to ensure future success.
F1's race to secure engine deals hots up
McLaren and Honda won 44 grands prix and eight world championships during their partnership during the 1980s and 90s.
"I think what is very clear is that McLaren needs to be supported and teamed in a full works effort with a major automotive manufacturer," Whitmarsh told a Vodafone phone-in on Tuesday.
"There is a lot of work between 2014 and 2015 for us undeniably, and [it will be] a tough challenge for the team.
"We're going to be doing all we can to win races with Mercedes this year and next, but inevitably moving to Honda in 2015 gives us a bedrock of being one of the big teams.
"[It] ensures that in the long term we have the resources, the correct structure and focus, to be successful.
"Clearly I'd like to win this weekend [at Monaco], and a bit more in the course of this year and next, but we're a team [with] 182 grand prix victories [and] in the long term we know we need to be putting together a programme that provides us with the platform to be successful every year in the foreseeable future."
Whitmarsh added that McLaren was not yet ready to abandon its 2013 world championship aspirations despite its poor start.
The team is already 102 points behind Red Bull in the constructors' championship, while Sebastian Vettel is more than 70 points clear of both Jenson Button and Sergio Perez in the drivers' standings.
Asked if the team was diverting more resources to its 2014 programme as a result of its troubled opening, Whitmarsh said: "No, it's actually probably less than we planned because we have to try harder on this year's car to be frank.
"It's still early enough in the season. We struggle to give up, and we have to believe we can get up there and get some good results.
"Sometimes that is a weakness in us, and we'll have to take stock of it later in the season, but at the moment we're very determined to make our car competitive and provide the sort of results we expect from ourselves."