Government ministers and the media have heavily criticized Rubiales over the gesture, with some saying it was unacceptable and an invasion of privacy.
FIFA's Disciplinary Committee informed Rubiales of the investigation, the association said in a news release. It said Rubiales' actions "may constitute violations" of its disciplinary code.
Rubiales was passing out gold medals to the team after its 1-0 victory Sunday over England when he kissed Hermoso.
Hermoso was heard telling teammates afterward in the locker room she "didn’t like it" in a video posted on Instagram and YouTube by the newspaper El Mundo and other media outlets.
She later was quoted played down the incident in a statement the federation sent to the Spanish news agency EFE, calling it a "mutual gesture that was totally spontaneous prompted by the huge joy of winning a world cup."
"The ‘presi’ and I have a great relationship, his behavior with all of us has always been 10 (out of 10) and this was a natural gesture of affection and gratitude," she was quoted as saying.
Asked about what happened on Spain’s COPE Radio station, Hermoso said: "I wish they created [controversy] involving someone else. I’m a world champion, and that’s what matters."
Others, however, quickly called out Rubiales.
Acting Gender Equality Minister Irene Montero said on X, formerly known as Twitter, that a nonconsensual kiss is a form of "sex violence." Acting Culture and Sports Minister Miquel Iceta told Radio Nacional de España that Rubiales' kissing Hermoso was unacceptable and asked him to apologize.
On Monday, Spain's El Pais newspaper published a column titled "Jenni didn’t like the kiss and we didn’t either." It described what happened as "an intrusion, an invasion of privacy, an aggression."
Rubiales dismissed critics as “idiots.”
“The kiss with Jenni? There are idiots everywhere. When two people have a moment of affection that means nothing more, you can’t listen to idiocy. We are the champions, that’s it,” he said according to Radio Marca.
FIFA said it will provide further information about the disciplinary proceedings once a final decision has been reached.
"FIFA reiterates its unwavering commitment to respecting the integrity of all individuals and strongly condemns any behavior to the contrary," the association said.