Marko, 80, referred to Mexican Perez's background when discussing his driver's inconsistent form this season.
Speaking after the Italian Grand Prix earlier this month, Red Bull motorsport adviser Marko said: “Let's remember that [Perez] is South American and so he is not as focused as Max Verstappen is or Sebastian Vettel was.”
Addressing Marko's comments ahead of this weekend's Singapore Grand Prix, Mercedes driver Hamilton, 38, said: “It is completely unacceptable. This is not something you just apologise for and it is all OK.
“Whilst we say there is no room for any type of discrimination in this sport - and there should be no room for it - to have leaders and people in his position making comments like this is not good for us moving forward.
“There are a lot of people in the background that really are combating these kind of things, but it is hard to manoeuvre if people at the top have mindsets which stop us from progressing.
“But it is not my team and not how we move as a team. We still have a lot of work to do to make this a more inclusive environment.”
Perez and teammate Verstappen shared two victories from the opening four races, but the latter is unbeaten since the fifth round in Miami.
Perez, 145 points behind Verstappen in the standings, said: “I had a private conversation with Helmut and he did apologise. To me, that was the main thing.
“Basically, we move on. I have a personal relationship with him. Knowing the person helps a lot, because I know he doesn't mean it that way. Personally, I didn't get offended.”