The Austrian, a former racer who was a close friend of Red Bull's late owner Dietrich Mateschitz, made the initial remarks on the energy drink company's Servus TV following last weekend's Italian Grand Prix.
"We know that he has problems in qualifying, he has fluctuations in form, he is South American and he is just not as completely focused in his head as Max (Verstappen) is or as Sebastian (Vettel)," said Marko.
It was not the first time Marko has referred to Perez as a South American, although the Mexican comes from Guadalajara which is geographically in North America.
South America has also produced more Formula 1 world champions than any country other than Britain.
The website on Friday reported Marko as saying: "It wasn't meant that way. I meant that a Mexican has a different mentality than a German or a Dutchman. But who knows, maybe it’s controlled."
It was reported by @RBR_Daily that Marko later apologised for the remarks.
The initial comments made headlines in Mexico and across the internet.
While Marko is a key figure who attends races in Red Bull Racing uniform, he reports to the energy drink company and is not an employee of the British-based champions, who had no immediate comment.
"This cannot keep happening to Sergio Perez," declared www.the-race.com on Friday.
"He deserves better than to have to grin and bear derogatory remarks from a senior figure in Red Bull’s Formula 1 organisation. The way Helmut Marko talks about him needs to stop."
The @RBR_Daily feed on social media site X, previously Twitter, condemned Marko's comments in a statement to its 35,000 followers.
"Such comments will not be tolerated. A racial stereotype was used to criticise his performance which is absolutely disgraceful and inexcusable," it said.
Perez joined Red Bull in 2021 with the team looking for a solid teammate to support Dutch driver Max Verstappen, who is now heading for his third world title. Germany's Vettel won four for Red Bull from 2010-13.
The Mexican has won six races, two of them this season, and has a contract for 2024.
He is second overall in the championship but is 145 points behind Verstappen after 14 of 22 races and his future after 2024 remains uncertain.
Marko did compliment Perez for finishing second in Italy last weekend, a race that handed Verstappen a record 10th win in a row.
"He had a very good race. Overtaking three drivers, in George Russell and the Ferraris, was not easy," said the Austrian.
