After the Italian Grand Prix, Marko, Red Bull's motorsport consultant, said Pérez's ethnicity was to blame for his poor form this year.
"We know that he has problems in qualifying, he has fluctuations in form," Marko said. "He is South American and he is just not as completely focused in his head as Max [Verstappen] is or as Sebastian [Vettel]."
The comments caused a huge stir on social media, and Marko was forced to issue a public apology, also saying sorry to Pérez in private.
Hamilton, F1's only Black driver, said it shows how far the championship still has to come in tackling discrimination.
"It's completely unacceptable what he said," Hamilton told Sky Sports.
"Whilst we say there is no room for any type of discrimination within this sport which 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 forwards.
"I think it just highlights, firstly, the work that still needs to be done. There are a lot of people in the background that really are trying to combat these sorts of things, but it's hard to manoeuvre if there are people in the top that have those sort of mindsets, that just stop us from progressing. Not surprised, to be honest."
The comments placed huge pressure on the Red Bull team to issue a statement condemning Marko, but the Austrian is not officially employed by the company.
However, he is one of the people most closely associated with the Formula One team and brand.
Marko's apology statement was put out on Red Bull-owned TV channel Servus, but the F1 team did not put out anything of its own.
On the apology, Hamilton said: "I don't know what was said beyond, that's something to ask Checo, but I think this is not something that you just apologise [for] and it's all OK. I think there needs to be more done.
"Teams, when they've had individuals, particularly drivers, make comments but [also] some individuals in the background -- they usually are removed or at least they put out a quote and say they don't support that sort of thing. So it is interesting that they haven't done so for this one, but it's not my team and it's not how we move as a team.
"It just shows how important it is that we continue to do the work. The work that I'm trying to do with my team and with the sport. We still have a lot of work to do moving forward to make sure that this is a more inclusive environment."