Mexican politician Antonio Perez Garibay made a beeline for Schumacher after he criticised his son's below-par season with Red Bull.
Former F1 driver Schumacher came out as gay earlier this year after informing fans that he was in a relationship with a man.
He received a barrage of supportive messages from important figures in the sport including seven-time world champion Lewis Hamilton.
However, Perez Garibay appeared to use it as a means to hit back at Schumacher.
He told ESPN's Racing podcast: "There's one driver, or a journalist, used to be a Formula 1 driver, who first claimed that Checo had been kicked out of Red Bull, and then the next week he came out of the closet.
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"I don't know, maybe he's in love with Checo? You don't know anymore if he's a journalist, a woman or a man. But even his words are questionable, not even because of Checo, but because of what his (ex) wife said about him."
Perez Garibay was referring to comments from Schumacher's ex-wife who claimed to have no knowledge of his homosexuality before describing it as a 'stab in the heart.'
The Mexican's comments have been roundly condemned with German sports outlet Bild labelling them as 'completely unacceptable.'
Schumacher, however, took a more measured approach when responding to the Mexican in a post on Instagram.
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Writing in his native German, the 49-year-old said: "I would also stand 100 percent behind my son and try to help. That's what you do as a father.
"As for the style, I would approach it differently, but we know Mr Perez with all his emotions. That's why I'm not angry with him.
"However, I believe results on the track would be a better argument."
Perez has struggled for form this season which coincided with him signing a new contract with Red Bull.
He is currently eighth in the drivers' standings with just 151 points and three rounds to go in the season.
Red Bull have had to rely on team-mate Max Verstappen in the race to top the constructor championship, with the Dutchman closing in on a fourth world title.
Perez, who avoided the axe this summer, faces an anxious wait to see what his role will be, if at all, with Red Bull next season.