The Policlinica Tibidabo clinic in Barcelona allegedly offers pills and psychiatric therapy to people who believe they can become straight.
According to the Spanish El Pais newspaper, many of the clinic’s patients belong to religions which do not accept homosexuality.
A spokeswoman for the regional government’s health department told AFP: "An investigation has been opened into this clinic.
"We do not consider homosexuality as an illness, far from it."
She added the clinic would be the subject of a month-long investigation and could face fines if such treatments were being carried out.
Spain legalised homosexuality in 1979. In 2005, it became the third European country to legalise gay marriage.