There have been rumours that McLaren will look elsewhere in the coming seasons with the team now having to pay for their engines from next season.
However, Whitmarsh has confirmed that McLaren intend to continue their 18-year partnership with the German engine manufacturers.
"It is going to be McLaren Mercedes for quite a few years to come," he told the Daily Mail.
"It is a good partnership and it works well. We've been together for 18 years and it is going to continue for quite a few years to come.
"I think we have got a very good deal with them, but I think more importantly than that is we have got a good partnership."
McLaren have struggled against Red Bull this season and are currently third in the constructors' championship.