In the wake of a season where Red Bull driver Perez has failed to match the performances of team-mate Max Verstappen, Marko has not held back in his criticisms of the Mexican at times.
But in remarks he made to Red Bull's own channel ServusTV earlier this week, he stepped up the rhetoric when he suggested that Perez's nationality was to blame for some of his woes.
"We know that he has problems in qualifying, he has fluctuations in form," said Marko.
"He is South American and he is just not as completely focused in his head as Max (Verstappen) is or as Sebastian (Vettel)."
As well as Marko's comments being an insult to Perez and all South Americans, it also caused a stir in Mexico because the country is officially in North America.
Amid ongoing speculation about Perez's future at the team, and growing discontent over Marko's comments, ServusTV issued a statement on behalf of Marko on Friday apologising for what he said.
The statement, posted on its website, said: "I would like to apologise for my offensive remark and want to make it absolutely clear that I do not believe that we can generalise about the people from any country, any race, any ethnicity.
"I was trying to make a point that Checo has fluctuated in his performance this year, but it was wrong to attribute this to his cultural heritage."
Perez has a contract to remain at Red Bull for 2024 but there has been mounting speculation about whether or not he will remain in the squad beyond then.
The Mexican dropped the first hint about a potential future elsewhere after the Italian GP when he suggested that critical to him remaining was the belief that he could contribute to team success.
"With the season we've had it's important in the next few races that I also want to be in an environment in which I feel like I can contribute," he told Spanish channel DAZN.
"And if that place in 2024 isn't here we have to look for other alternatives. But right now my main focus is being here, winning more races, continuing to win championships with Red Bull.
"I have a contract until next year, so some time next year we will sit down and talk."
