Regional health minister Mauro Poggia asked a commission overseeing health professionals and patients' rights in the canton to open an investigation into the practice of Dr Jean-Yves Henry, he told the Le Courrier daily in an interview published Wednesday.
"For him it would seem that homosexuality is an illness to cure," Poggia said. "This element is enough to justify opening an investigation."
The move has been sparked by social media uproar over an article Henry wrote in 2009 in which he said that homosexuality is "not a pathology but a special symptom" seen in "border-line" and other patients.
The 71-year-old general practitioner and naturopath describes attraction to a person of the same sex as a "symptom", for which homeopathy can offer a "remedy" and recommends different methods for boys and girls.
Contacted by Swiss public broadcaster RTS Tuesday, he was unrepentant.
"Homosexuality is a symptom like any other, like having a headache or hay fever," he said. "I don't understand what the problem is."
As well as his practice, Henry runs a subscriber-only website on alternative medicine.
An undated addendum on the website where his article was published appears to take issue with the recent media coverage, saying that homosexuality is one of 64,000 "symptoms" that Henry and his colleagues evaluate in their work.
The note stressed that the page on homosexuality had first and foremost been aimed at "making our students think about the relationship between medical remedies and behavioural symptoms".
The probe will examine whether the opinions Henry expressed are independent of his medical practice and whether he has endangered his patients or practised illegal medicine, according to Poggia.
The president of the Geneva medical practitioners' association, Michel Matter, told RTS that Henry seemed to be guilty of "charlatanism".
Swiss gay rights are planning to take legal action.